Variant report

Variant	rs171080
Chromosome Location	chr3:156555500-156555501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156391465..156393079-chr3:156555230..156557059,2	MCF-7	breast:
2	chr3:156404124..156405692-chr3:156554376..156556285,2	K562	blood:
3	chr3:156552175..156554345-chr3:156554997..156556879,2	MCF-7	breast:
4	chr3:156554023..156556645-chr3:156558836..156560959,2	MCF-7	breast:
5	chr3:156542736..156546133-chr3:156552439..156555764,4	K562	blood:
6	chr3:156541425..156545674-chr3:156551760..156556464,6	K562	blood:

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000197980	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs11710516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11717138	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11927500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13321802	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1355280	1.00[CHB][hapmap]
rs1430412	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1510270	1.00[CHB][hapmap]
rs16826858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16826864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16826899	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16826906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16826948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs171077	0.83[ASN][1000 genomes]
rs180746	0.83[ASN][1000 genomes]
rs180747	1.00[CHB][hapmap]
rs182936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs184677	1.00[CHB][hapmap]
rs193198	1.00[CHB][hapmap]
rs193423	1.00[CHB][hapmap]
rs2054881	1.00[CHB][hapmap]
rs2129909	1.00[CHB][hapmap]
rs237246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2633815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2665390	1.00[CHB][hapmap]
rs28661978	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2874490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2874491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344005	1.00[CHB][hapmap]
rs344006	1.00[CHB][hapmap]
rs344008	1.00[CHB][hapmap]
rs344009	1.00[CHB][hapmap]
rs344010	1.00[CHB][hapmap]
rs344011	1.00[CHB][hapmap]
rs344012	1.00[CHB][hapmap]
rs344013	1.00[CHB][hapmap]
rs344014	1.00[CHB][hapmap]
rs344015	1.00[CHB][hapmap]
rs344016	1.00[CHB][hapmap]
rs344017	1.00[CHB][hapmap]
rs344023	0.83[ASN][1000 genomes]
rs344047	0.83[ASN][1000 genomes]
rs344048	0.83[ASN][1000 genomes]
rs344049	0.83[ASN][1000 genomes]
rs344050	0.83[ASN][1000 genomes]
rs344052	1.00[CHB][hapmap]
rs344053	1.00[CHB][hapmap]
rs344054	1.00[CHB][hapmap]
rs344055	1.00[CHB][hapmap]
rs344058	1.00[CHB][hapmap]
rs344059	1.00[CHB][hapmap]
rs344060	1.00[CHB][hapmap]
rs344061	1.00[CHB][hapmap]
rs344062	1.00[CHB][hapmap]
rs344063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344064	1.00[CHB][hapmap]
rs344065	1.00[CHB][hapmap]
rs344066	1.00[CHB][hapmap]
rs344068	1.00[CHB][hapmap]
rs344069	1.00[CHB][hapmap]
rs344070	1.00[CHB][hapmap]
rs344074	1.00[CHB][hapmap]
rs344076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344085	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344088	0.89[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344089	0.90[ASN][1000 genomes]
rs344090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344093	0.83[ASN][1000 genomes]
rs3796172	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs414683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs419287	1.00[CHB][hapmap]
rs427384	1.00[CHB][hapmap]
rs4429586	1.00[CHB][hapmap]
rs4441614	0.84[ASN][1000 genomes]
rs4680304	0.84[ASN][1000 genomes]
rs491423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55850252	0.84[ASN][1000 genomes]
rs58207863	0.84[ASN][1000 genomes]
rs59244547	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441095	1.00[CHB][hapmap]
rs6441099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6441100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6441103	0.89[ASN][1000 genomes]
rs6441104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6763644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6774702	0.84[ASN][1000 genomes]
rs6786167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6787535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6787952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6792917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6795327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6795516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6802042	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6802511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7426821	0.84[ASN][1000 genomes]
rs7609851	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7618306	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7621699	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7630909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7635521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7640994	0.89[ASN][1000 genomes]
rs7650127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs978108	1.00[CHB][hapmap]
rs9810194	0.84[ASN][1000 genomes]
rs9823112	1.00[CHB][hapmap]
rs9841269	0.84[ASN][1000 genomes]
rs9847692	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9861359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9878709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156545000-156559600	Weak transcription	Pancreas	Pancrea
2	chr3:156545800-156558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:156554000-156558200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:156554400-156555600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:156554400-156555600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:156554400-156555600	Enhancers	NHDF-Ad	bronchial
7	chr3:156554400-156555800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:156554400-156558400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:156554400-156561000	Weak transcription	Aorta	Aorta
10	chr3:156555000-156555600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:156555000-156555800	Enhancers	A549	lung
12	chr3:156555200-156556800	Enhancers	HepG2	liver
13	chr3:156555400-156555600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:156555400-156558800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:156555400-156560400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:156555400-156560400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:156555400-156560400	Weak transcription	Osteobl	bone
18	chr3:156555400-156560800	Weak transcription	Muscle Satellite Cultured Cells	--

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