Variant report

Variant	rs7644273
Chromosome Location	chr3:105115736-105115737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105115312..105118076-chr3:105118161..105120646,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10049426	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036582	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036583	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10511243	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10933816	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10933817	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488994	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491980	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494392	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695118	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13062366	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13064396	1.00[ASN][1000 genomes]
rs13092811	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13093663	0.95[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13097669	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100098	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438538	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438541	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1530069	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898654	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178407	0.86[ASW][hapmap];0.91[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.80[MEX][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2196745	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2399045	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28670976	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895299	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426702	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4894831	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894924	0.88[CHD][hapmap]
rs57834585	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437587	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6437589	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66805489	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6767277	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767814	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769302	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779807	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780238	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796658	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6806304	0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7431531	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7615005	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629589	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641185	0.82[CHD][hapmap]
rs7647011	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7649033	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288802	0.81[ASW][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288805	0.82[AFR][1000 genomes]
rs934856	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975574	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9842028	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851952	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9870921	0.87[CHD][hapmap]
rs9883620	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9883799	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105105000-105116800	Weak transcription	Aorta	Aorta
2	chr3:105107000-105116800	Weak transcription	Osteobl	bone
3	chr3:105107000-105119400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:105108000-105118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:105110800-105120000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:105113400-105116000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:105113400-105116600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:105113400-105116600	Weak transcription	NH-A	brain
9	chr3:105113400-105116800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:105113400-105116800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:105113400-105116800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:105113400-105121200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:105113400-105121400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:105113400-105122400	Weak transcription	Primary B cells from cord blood	blood
15	chr3:105113800-105116800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:105113800-105116800	Weak transcription	A549	lung
17	chr3:105113800-105117600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:105113800-105118000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:105114000-105116800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:105114000-105116800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:105114000-105116800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:105114000-105118600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:105114400-105116800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:105114600-105123400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:105115600-105115800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:105115600-105115800	Enhancers	Brain Anterior Caudate	brain
27	chr3:105115600-105116800	Weak transcription	Brain Angular Gyrus	brain

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