Variant report

Variant	rs13025791
Chromosome Location	chr2:128388790-128388791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128388188..128389976-chr2:128397282..128399225,3	MCF-7	breast:
2	chr2:128386978..128389867-chr2:128392766..128396164,5	MCF-7	breast:
3	chr2:128385318..128388983-chr2:128393086..128394739,3	MCF-7	breast:
4	chr2:128387080..128389116-chr2:128389708..128392331,3	MCF-7	breast:
5	chr2:128388582..128390159-chr2:128390369..128392220,2	K562	blood:
6	chr2:128386610..128389542-chr2:128567624..128570008,2	MCF-7	breast:
7	chr2:128349017..128351644-chr2:128387621..128389792,2	MCF-7	breast:
8	chr2:128388233..128390478-chr2:128396235..128397787,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169994	Chromatin interaction
ENSG00000072163	Chromatin interaction
ENSG00000136709	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10928774	0.94[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10928775	0.94[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11675513	0.87[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11684148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686946	0.94[CEU][hapmap];0.80[CHD][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11691981	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12052293	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12052654	0.93[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12053039	0.93[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12053248	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12999486	1.00[ASW][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs13004906	0.94[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13006453	0.94[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13015157	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13025959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034190	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17261964	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252610	0.92[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs2253005	0.92[ASN][1000 genomes]
rs2255161	0.94[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2264727	0.80[ASN][1000 genomes]
rs34190613	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34280534	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36108975	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4662585	0.89[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4662748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62156627	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs705092	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs777432	0.92[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs777433	0.92[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs930139	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011937	chr2:128295320-128405921	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1008294	chr2:128295320-128420654	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1007207	chr2:128295320-128429775	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1003004	chr2:128295320-128474326	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv1008457	chr2:128299079-128405921	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1009514	chr2:128299079-128420654	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1006421	chr2:128299079-128473079	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv1004877	chr2:128299079-128479640	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv875015	chr2:128305196-128495645	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1001624	chr2:128306660-128420654	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv875016	chr2:128330458-128401091	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv875017	chr2:128330458-128445585	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv875018	chr2:128330458-128465547	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv518085	chr2:128334413-128404860	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv583037	chr2:128334470-128401091	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv875019	chr2:128340855-128408170	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv875020	chr2:128340855-128445585	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv875021	chr2:128340855-128465547	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
19	nsv470482	chr2:128350808-128465547	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
20	esv3368061	chr2:128375044-128672849	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
21	nsv875022	chr2:128378563-128405721	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv875023	chr2:128378563-128407499	Bivalent Enhancer Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	nsv875024	chr2:128378563-128408170	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
24	nsv875025	chr2:128378563-128409419	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
25	nsv875026	chr2:128378563-128445585	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
26	nsv428726	chr2:128387756-128539894	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
27	nsv517532	chr2:128387937-128404860	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv875027	chr2:128387937-128408170	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
29	nsv875028	chr2:128387937-128445585	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13025791	GPR17	cis	cerebellum	SCAN
rs13025791	BIN1	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128359200-128395200	Strong transcription	Duodenum Mucosa	Duodenum
2	chr2:128371000-128391600	Strong transcription	Fetal Intestine Large	intestine
3	chr2:128371400-128390800	Strong transcription	Fetal Intestine Small	intestine
4	chr2:128376600-128391200	Weak transcription	HSMMtube	muscle
5	chr2:128378400-128392000	Enhancers	Primary B cells from peripheral blood	blood
6	chr2:128378400-128393600	Genic enhancers	Dnd41	blood
7	chr2:128381800-128391000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:128382800-128391000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:128383000-128391800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:128384400-128392400	Enhancers	Right Ventricle	heart
11	chr2:128385200-128389200	Strong transcription	Colonic Mucosa	Colon
12	chr2:128385400-128388800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:128385800-128388800	Enhancers	Spleen	Spleen
14	chr2:128386200-128396000	Enhancers	Fetal Thymus	thymus
15	chr2:128386400-128395600	Enhancers	Primary B cells from cord blood	blood
16	chr2:128386600-128391200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:128386600-128394400	Enhancers	Fetal Heart	heart
18	chr2:128387000-128389000	Enhancers	Stomach Smooth Muscle	stomach
19	chr2:128387000-128392600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:128387400-128392600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:128387400-128396400	Enhancers	Placenta	Placenta
22	chr2:128387600-128389000	Enhancers	Primary hematopoietic stem cells	blood
23	chr2:128387600-128389000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:128387600-128389000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr2:128387600-128389200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:128387600-128392200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:128387600-128392400	Enhancers	Right Atrium	heart
28	chr2:128387800-128389800	Enhancers	Lung	lung
29	chr2:128387800-128391600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:128388000-128388800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:128388000-128388800	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:128388000-128389800	Enhancers	Colon Smooth Muscle	Colon
33	chr2:128388000-128393200	Enhancers	Left Ventricle	heart
34	chr2:128388000-128394600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:128388000-128394800	Enhancers	Adipose Nuclei	Adipose
36	chr2:128388000-128395000	Enhancers	Primary T cells fromperipheralblood	blood
37	chr2:128388200-128388800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:128388200-128389400	Enhancers	Primary T cells from cord blood	blood
39	chr2:128388200-128391000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:128388200-128393600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:128388400-128388800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:128388400-128388800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:128388400-128389400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:128388600-128389400	Enhancers	Esophagus	oesophagus
45	chr2:128388600-128393800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:128388600-128395000	Enhancers	Primary T helper cells PMA-I stimulated	--

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