Variant report

Variant	rs344070
Chromosome Location	chr3:156443980-156443981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156443136..156445606-chr3:156450244..156452824,2	MCF-7	breast:
2	chr3:156443560..156446468-chr3:156533893..156536827,2	K562	blood:
3	chr3:156443661..156446462-chr3:156462331..156464626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs11710516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11927500	1.00[CHB][hapmap]
rs13321802	1.00[CHB][hapmap]
rs1355280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1397194	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397195	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510269	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1510270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs168245	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16826858	1.00[CHB][hapmap]
rs16826864	1.00[CHB][hapmap]
rs16826899	1.00[CHB][hapmap]
rs16826906	1.00[CHB][hapmap]
rs168295	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs171077	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs171080	1.00[CHB][hapmap]
rs180746	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs180747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs182935	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs182936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs184677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858229	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs186928	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs193423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054881	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]
rs2129909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136691	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2136692	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs237245	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2633815	1.00[CHB][hapmap]
rs2665390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2874490	1.00[CHB][hapmap]
rs343991	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343992	1.00[CHB][hapmap]
rs343995	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343998	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344001	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs344009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344014	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344023	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344029	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs344032	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344047	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344048	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344049	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344050	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs344062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs344064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344069	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]
rs344074	1.00[CHB][hapmap]
rs344076	1.00[CHB][hapmap]
rs344078	1.00[CHB][hapmap]
rs344081	1.00[CHB][hapmap]
rs344083	1.00[CHB][hapmap]
rs344086	1.00[CHB][hapmap]
rs344090	1.00[CHB][hapmap]
rs344091	1.00[CHB][hapmap]
rs344092	1.00[CHB][hapmap]
rs345987	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs414683	1.00[CHB][hapmap]
rs419287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4279048	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4429586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4679784	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680297	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4680298	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4680299	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs491423	1.00[CHB][hapmap]
rs5012666	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441089	0.83[AMR][1000 genomes]
rs6441092	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441093	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441094	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441099	1.00[CHB][hapmap]
rs6441100	1.00[CHB][hapmap]
rs6763644	1.00[CHB][hapmap]
rs6786167	1.00[CHB][hapmap]
rs6787535	1.00[CHB][hapmap]
rs6787952	1.00[CHB][hapmap]
rs6792917	1.00[CHB][hapmap]
rs6795327	1.00[CHB][hapmap]
rs6795516	1.00[CHB][hapmap]
rs6799457	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7609851	1.00[CHB][hapmap]
rs7630909	1.00[CHB][hapmap]
rs7635521	1.00[CHB][hapmap]
rs7640593	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7650127	1.00[CHB][hapmap]
rs871232	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs871233	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs907063	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs931990	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs978108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978109	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833951	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9861359	1.00[CHB][hapmap]
rs9877043	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9878709	1.00[CHB][hapmap]

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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156423000-156445800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:156424200-156445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:156426600-156446000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:156428600-156445200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:156433800-156445000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:156435200-156444800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:156436200-156446200	Weak transcription	Gastric	stomach
8	chr3:156436600-156445800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:156437000-156446000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:156437200-156446000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:156437200-156447400	Weak transcription	Pancreas	Pancrea
12	chr3:156438800-156444400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:156439000-156447400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:156439400-156445800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:156439400-156446600	Enhancers	Stomach Mucosa	stomach
16	chr3:156439600-156451800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:156439800-156445800	Weak transcription	A549	lung
18	chr3:156440400-156450200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:156441200-156444000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:156441200-156445200	Weak transcription	Left Ventricle	heart
21	chr3:156441200-156445200	Weak transcription	Right Atrium	heart
22	chr3:156441200-156447400	Weak transcription	Lung	lung
23	chr3:156441400-156444000	Weak transcription	Esophagus	oesophagus
24	chr3:156441400-156445200	Weak transcription	GM12878-XiMat	blood
25	chr3:156441400-156445800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:156441400-156445800	Weak transcription	NHLF	lung
27	chr3:156441600-156444000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:156441600-156444600	Weak transcription	HSMMtube	muscle
29	chr3:156441600-156445800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:156441800-156444600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:156441800-156444600	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr3:156441800-156445200	Weak transcription	NHDF-Ad	bronchial
33	chr3:156441800-156445400	Strong transcription	HSMM	muscle
34	chr3:156442400-156444400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:156442400-156445800	Weak transcription	Osteobl	bone
36	chr3:156442800-156444400	Enhancers	HMEC	breast
37	chr3:156442800-156444400	Strong transcription	NH-A	brain
38	chr3:156442800-156447800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:156443000-156444200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr3:156443000-156444400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr3:156443000-156446000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:156443200-156444800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:156443200-156445800	Weak transcription	Fetal Intestine Large	intestine
44	chr3:156443400-156444400	Enhancers	NHEK	skin
45	chr3:156443400-156445000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:156443600-156444200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:156443800-156444400	Enhancers	Small Intestine	intestine

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