Variant report

Variant	rs9967820
Chromosome Location	chr2:179349227-179349228
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179347333..179349438-chr2:179354619..179356582,3	MCF-7	breast:
2	chr2:179343596..179347603-chr2:179348406..179354533,12	MCF-7	breast:
3	chr2:179314116..179315931-chr2:179347973..179349774,2	MCF-7	breast:
4	chr2:179348931..179350689-chr2:179372873..179374989,2	K562	blood:

Variant related genes	Relation type
ENSG00000116095	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10188593	0.92[CEU][hapmap]
rs10207436	1.00[JPT][hapmap]
rs10930831	1.00[JPT][hapmap]
rs11688081	0.91[YRI][hapmap]
rs12052983	1.00[JPT][hapmap]
rs12615347	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13382684	0.82[AMR][1000 genomes]
rs13411588	1.00[JPT][hapmap]
rs1559908	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16866334	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16866342	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1863671	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1967327	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs1978580	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2016615	0.83[ASN][1000 genomes]
rs2042996	0.84[JPT][hapmap]
rs2059691	0.85[JPT][hapmap]
rs2114582	0.95[JPT][hapmap]
rs2249737	0.85[JPT][hapmap]
rs2288320	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs2288322	1.00[JPT][hapmap]
rs2288323	0.88[ASW][hapmap]
rs2303536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2303537	1.00[JPT][hapmap]
rs33998881	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731750	0.84[JPT][hapmap]
rs3731754	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3752689	1.00[JPT][hapmap]
rs3769866	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4019558	0.91[YRI][hapmap]
rs4404314	0.91[YRI][hapmap]
rs4894017	0.90[JPT][hapmap]
rs4894020	1.00[JPT][hapmap]
rs60488846	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704545	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6726043	0.81[ASN][1000 genomes]
rs6739142	1.00[JPT][hapmap]
rs6753709	1.00[JPT][hapmap]
rs7575643	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7577862	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7587593	0.81[ASN][1000 genomes]
rs7588593	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589679	1.00[JPT][hapmap]
rs7598228	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7600176	1.00[JPT][hapmap]
rs7602597	0.83[GIH][hapmap];0.80[ASN][1000 genomes]
rs8179648	0.80[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9288019	1.00[JPT][hapmap]
rs957875	0.84[JPT][hapmap]
rs967507	1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179346000-179350200	Enhancers	Small Intestine	intestine
2	chr2:179346000-179355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:179346200-179350000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:179346400-179349400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr2:179346400-179349400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr2:179346400-179355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:179346400-179358600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:179346400-179387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:179346600-179349600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr2:179346600-179350200	Enhancers	Stomach Mucosa	stomach
11	chr2:179346600-179350400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:179346600-179351000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:179346600-179356200	Weak transcription	Colonic Mucosa	Colon
14	chr2:179346600-179358600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:179346800-179349400	Enhancers	Brain Anterior Caudate	brain
16	chr2:179346800-179349800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:179346800-179349800	Enhancers	K562	blood
18	chr2:179346800-179350200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:179346800-179350200	Enhancers	Liver	Liver
20	chr2:179346800-179350200	Enhancers	Brain Substantia Nigra	brain
21	chr2:179346800-179350200	Enhancers	Right Ventricle	heart
22	chr2:179346800-179350400	Enhancers	Colon Smooth Muscle	Colon
23	chr2:179347000-179350800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:179347200-179349400	Weak transcription	NHLF	lung
25	chr2:179347200-179349600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:179347200-179349600	Enhancers	HepG2	liver
27	chr2:179347200-179349800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:179347200-179349800	Enhancers	Left Ventricle	heart
29	chr2:179347200-179350200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:179347200-179350200	Enhancers	Right Atrium	heart
31	chr2:179347200-179350200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:179347200-179350200	Enhancers	A549	lung
33	chr2:179347200-179350400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:179347200-179354400	Weak transcription	Placenta	Placenta
35	chr2:179347200-179355800	Weak transcription	HMEC	breast
36	chr2:179347200-179356000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:179347200-179356000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:179347200-179358600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:179347200-179358600	Weak transcription	NHEK	skin
40	chr2:179347200-179358800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:179347400-179349800	Enhancers	Ovary	ovary
42	chr2:179347400-179350200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr2:179347400-179350400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:179347400-179350400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:179347400-179350400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr2:179347400-179350600	Weak transcription	HSMM	muscle
47	chr2:179347400-179350800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:179347400-179350800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:179347400-179351000	Weak transcription	Lung	lung
50	chr2:179347400-179354600	Weak transcription	Rectal Mucosa Donor 29	rectum

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