Variant report

Variant	rs4662750
Chromosome Location	chr2:128392547-128392548
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128391814..128393751-chr2:128458053..128460441,2	MCF-7	breast:
2	chr2:128367073..128368593-chr2:128390549..128393243,2	K562	blood:
3	chr2:128283737..128286203-chr2:128392070..128394407,2	MCF-7	breast:
4	chr2:128389876..128393259-chr2:128457359..128460267,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIMS2-1	chr2:128391285-128394251	NONHSAT074176

Variant related genes	Relation type
ENSG00000169994	Chromatin interaction
ENSG00000163166	Chromatin interaction
ENSG00000173349	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1835431	0.83[AMR][1000 genomes]
rs2009707	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2245297	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2248519	0.83[AMR][1000 genomes]
rs2254680	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2255177	0.83[CHD][hapmap]
rs2255178	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4662743	0.88[ASW][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap]
rs4662749	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6715608	0.82[MEX][hapmap]
rs777435	0.92[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs777437	0.93[GIH][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4662750	SAP130	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128359200-128395200	Strong transcription	Duodenum Mucosa	Duodenum
2	chr2:128378400-128393600	Genic enhancers	Dnd41	blood
3	chr2:128386200-128396000	Enhancers	Fetal Thymus	thymus
4	chr2:128386400-128395600	Enhancers	Primary B cells from cord blood	blood
5	chr2:128386600-128394400	Enhancers	Fetal Heart	heart
6	chr2:128387000-128392600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:128387400-128392600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:128387400-128396400	Enhancers	Placenta	Placenta
9	chr2:128388000-128393200	Enhancers	Left Ventricle	heart
10	chr2:128388000-128394600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:128388000-128394800	Enhancers	Adipose Nuclei	Adipose
12	chr2:128388000-128395000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:128388200-128393600	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:128388600-128393800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:128388600-128395000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:128388800-128392600	Enhancers	Fetal Muscle Leg	muscle
17	chr2:128388800-128395000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:128389000-128394800	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr2:128389800-128395200	Enhancers	Primary T cells from cord blood	blood
20	chr2:128390000-128393000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:128390000-128397200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr2:128390400-128395400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:128390800-128392600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:128390800-128393800	Enhancers	Lung	lung
25	chr2:128390800-128398400	Genic enhancers	Fetal Intestine Small	intestine
26	chr2:128391000-128393000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:128391000-128393800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:128391200-128392800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:128391200-128393400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:128391200-128395600	Enhancers	Fetal Muscle Trunk	muscle
31	chr2:128391400-128393000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:128391400-128393800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:128391400-128394600	Weak transcription	Thymus	Thymus
34	chr2:128391400-128395000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:128391400-128396200	Genic enhancers	Spleen	Spleen
36	chr2:128391600-128392600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr2:128391600-128392800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:128391600-128393000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:128391600-128393400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:128391600-128394400	Weak transcription	HUVEC	blood vessel
41	chr2:128391600-128395000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:128391600-128395000	Weak transcription	Brain Anterior Caudate	brain
43	chr2:128391600-128397200	Genic enhancers	Fetal Intestine Large	intestine
44	chr2:128391800-128393000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:128391800-128393200	Enhancers	Stomach Smooth Muscle	stomach
46	chr2:128391800-128394200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:128391800-128394400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:128391800-128394600	Weak transcription	NHLF	lung
49	chr2:128391800-128394800	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:128392000-128392600	Genic enhancers	Primary B cells from peripheral blood	blood

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