Variant report

Variant	rs957875
Chromosome Location	chr2:179384417-179384418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:179382793-179385336	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179377244..179379642-chr2:179381924..179384722,3	K562	blood:

Variant related genes	Relation type
TTN-AS1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1001238	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10207436	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10930831	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs12052983	0.90[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs12693162	0.88[CEU][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13411588	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1559908	0.84[JPT][hapmap]
rs1560221	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866334	0.84[JPT][hapmap]
rs16866342	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs16866400	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs16866420	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1978580	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2016615	0.81[ASN][1000 genomes]
rs2042995	1.00[CEU][hapmap]
rs2042996	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2114582	0.81[CHB][hapmap]
rs2163009	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2249737	0.86[CHB][hapmap]
rs2288322	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2288571	0.81[JPT][hapmap]
rs2303536	0.84[JPT][hapmap]
rs2303537	0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2303838	0.85[JPT][hapmap]
rs2366751	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2472751	0.94[CEU][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2742351	0.82[CHB][hapmap]
rs35504893	0.89[ASN][1000 genomes]
rs36113194	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3731746	0.85[JPT][hapmap]
rs3731750	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3731754	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3752689	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs3769864	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769866	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3813250	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3820978	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3829746	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4894020	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4894029	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894030	0.82[CHB][hapmap]
rs6704545	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs6712785	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6723399	0.96[ASN][1000 genomes]
rs6735077	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739142	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs6753709	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs7575643	0.84[JPT][hapmap]
rs7577862	0.84[JPT][hapmap]
rs7589679	0.81[JPT][hapmap]
rs7600176	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs8179648	0.90[JPT][hapmap]
rs890578	0.85[JPT][hapmap]
rs9288019	0.84[JPT][hapmap]
rs967507	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9808377	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9967820	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179346400-179387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:179359600-179387600	Weak transcription	Right Ventricle	heart
3	chr2:179359600-179387800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:179360800-179387800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:179361000-179387800	Weak transcription	Spleen	Spleen
6	chr2:179361400-179387200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:179365600-179387800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:179366000-179387600	Weak transcription	Fetal Brain Male	brain
9	chr2:179366000-179387800	Weak transcription	Small Intestine	intestine
10	chr2:179367600-179387600	Weak transcription	Fetal Kidney	kidney
11	chr2:179367800-179387600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:179368200-179387600	Weak transcription	Fetal Heart	heart
13	chr2:179368200-179387600	Weak transcription	Fetal Lung	lung
14	chr2:179368200-179387800	Weak transcription	Brain Substantia Nigra	brain
15	chr2:179368400-179387400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:179368400-179387600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:179368600-179387400	Weak transcription	A549	lung
18	chr2:179368600-179387600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:179368600-179387800	Weak transcription	Psoas Muscle	Psoas
20	chr2:179369000-179387400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:179369200-179387400	Weak transcription	K562	blood
22	chr2:179369200-179387600	Weak transcription	HUVEC	blood vessel
23	chr2:179370600-179387600	Weak transcription	Fetal Thymus	thymus
24	chr2:179371600-179387400	Weak transcription	HepG2	liver
25	chr2:179371600-179387600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:179372600-179387600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:179372800-179387800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:179373600-179388000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:179374000-179386600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:179376000-179387600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:179377000-179387400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:179378200-179387600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:179379200-179387400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:179379800-179387400	Weak transcription	GM12878-XiMat	blood
35	chr2:179379800-179387400	Weak transcription	NH-A	brain
36	chr2:179380000-179385800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:179380000-179387200	Weak transcription	HMEC	breast
38	chr2:179380000-179387400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:179380000-179387400	Weak transcription	Primary B cells from cord blood	blood
40	chr2:179380000-179387400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:179380000-179387400	Weak transcription	NHEK	skin
42	chr2:179380000-179387600	Weak transcription	NHDF-Ad	bronchial
43	chr2:179380200-179387400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:179380200-179387600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:179380400-179385600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:179382200-179384600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:179382400-179384600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:179382800-179387600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:179383200-179387600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:179383400-179387200	Weak transcription	Dnd41	blood

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