Variant report

Variant	rs13419955
Chromosome Location	chr2:128399414-128399415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:128399360-128399510	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128396263..128398888-chr2:128399161..128401002,2	MCF-7	breast:
2	chr2:128396660..128399808-chr2:128456748..128459804,3	K562	blood:
3	chr2:128399188..128401329-chr2:128456948..128459490,2	MCF-7	breast:
4	chr2:128280589..128286553-chr2:128394118..128400117,7	K562	blood:
5	chr2:128399168..128401965-chr2:128403212..128405574,3	MCF-7	breast:

No data

Variant related genes	Relation type
LIMS2	TF binding region
GPR17	TF binding region
ENSG00000072163	Chromatin interaction
ENSG00000163166	Chromatin interaction
ENSG00000173349	Chromatin interaction
ENSG00000144230	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10180750	0.86[CHD][hapmap]
rs1055199	0.93[ASN][1000 genomes]
rs13417920	0.86[CHD][hapmap]
rs13422424	0.86[CHD][hapmap]
rs1367403	0.86[CHD][hapmap]
rs2243934	0.81[CHB][hapmap]
rs2244655	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2288657	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[ASN][1000 genomes]
rs60245561	0.98[ASN][1000 genomes]
rs7584125	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:33 , 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
30	nsv875029	chr2:128395498-128465547	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases
31	nsv459252	chr2:128398840-128476484	Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases
32	nsv583038	chr2:128398840-128476484	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases
33	nsv875030	chr2:128399414-128495645	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128392000-128403000	Weak transcription	Brain Germinal Matrix	brain
2	chr2:128392200-128400400	Weak transcription	Brain Substantia Nigra	brain
3	chr2:128392400-128402000	Genic enhancers	Right Ventricle	heart
4	chr2:128392600-128400800	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:128393200-128400000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:128393800-128400800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:128394200-128401200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:128394400-128400000	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:128394800-128403000	Enhancers	Fetal Heart	heart
10	chr2:128395000-128407000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:128395200-128400000	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr2:128395400-128400000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
13	chr2:128395600-128403800	Genic enhancers	Stomach Smooth Muscle	stomach
14	chr2:128395800-128399800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:128395800-128400200	Weak transcription	Fetal Lung	lung
16	chr2:128395800-128400600	Weak transcription	Brain Anterior Caudate	brain
17	chr2:128395800-128404000	Weak transcription	Pancreas	Pancrea
18	chr2:128395800-128404600	Weak transcription	NHLF	lung
19	chr2:128396000-128400600	Strong transcription	Colon Smooth Muscle	Colon
20	chr2:128396000-128400800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:128396000-128401600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:128396000-128401600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:128396000-128404600	Weak transcription	Right Atrium	heart
24	chr2:128396200-128399800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:128396200-128401400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:128396200-128401600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:128396200-128402000	Strong transcription	Aorta	Aorta
28	chr2:128396200-128404200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:128396400-128406800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:128396600-128400800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:128396600-128400800	Genic enhancers	Spleen	Spleen
32	chr2:128396600-128401000	Enhancers	Primary B cells from cord blood	blood
33	chr2:128396600-128406800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:128396800-128399800	Strong transcription	Left Ventricle	heart
35	chr2:128396800-128401800	Enhancers	Fetal Muscle Trunk	muscle
36	chr2:128396800-128402400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:128396800-128403000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:128396800-128404200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:128396800-128408600	Weak transcription	Gastric	stomach
40	chr2:128397000-128399600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:128397000-128400200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr2:128397200-128400000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr2:128397400-128400000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr2:128397400-128400000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr2:128397400-128400400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr2:128397400-128400400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:128397400-128403200	Enhancers	Brain Cingulate Gyrus	brain
48	chr2:128397600-128400000	Flanking Active TSS	Fetal Thymus	thymus
49	chr2:128397600-128401600	Genic enhancers	Fetal Stomach	stomach
50	chr2:128397600-128401800	Enhancers	Fetal Muscle Leg	muscle

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