Variant report

Variant	rs9403139
Chromosome Location	chr6:140374362-140374363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:140373569..140374771-chr6:140762117..140763007,5	MCF-7	breast:
2	chr6:140368572..140371123-chr6:140374130..140376086,2	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10434888	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10872525	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1119397	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12174980	0.82[EUR][1000 genomes]
rs12175776	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12660474	0.82[EUR][1000 genomes]
rs12660560	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12662046	0.82[EUR][1000 genomes]
rs12662151	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12662747	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12663480	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12664312	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13191189	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs13204837	1.00[CEU][hapmap]
rs1324130	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1416289	0.87[CEU][hapmap]
rs1496112	0.82[EUR][1000 genomes]
rs1496113	0.82[EUR][1000 genomes]
rs1519592	0.82[EUR][1000 genomes]
rs1587171	0.82[EUR][1000 genomes]
rs1603348	0.82[EUR][1000 genomes]
rs1603349	0.82[EUR][1000 genomes]
rs17069736	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17069768	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17069852	0.84[EUR][1000 genomes]
rs17069854	0.84[EUR][1000 genomes]
rs2020197	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34358600	0.84[EUR][1000 genomes]
rs34753441	0.82[EUR][1000 genomes]
rs34984534	0.82[EUR][1000 genomes]
rs35332737	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35392782	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35465283	0.84[EUR][1000 genomes]
rs36074095	0.85[EUR][1000 genomes]
rs36126113	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56044741	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62431097	0.84[EUR][1000 genomes]
rs62431100	0.81[EUR][1000 genomes]
rs66460448	0.85[EUR][1000 genomes]
rs71562538	0.85[EUR][1000 genomes]
rs724061	0.90[CEU][hapmap]
rs72973906	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7758187	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs7761894	0.84[EUR][1000 genomes]
rs7763294	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9373256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9373258	0.84[EUR][1000 genomes]
rs9373259	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs9373260	0.83[EUR][1000 genomes]
rs9373261	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9373262	0.83[EUR][1000 genomes]
rs9376485	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9376493	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9376494	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9376495	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9376496	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376497	0.84[EUR][1000 genomes]
rs9376498	0.85[EUR][1000 genomes]
rs9376500	0.84[EUR][1000 genomes]
rs9376501	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9376502	0.84[EUR][1000 genomes]
rs9376503	0.83[EUR][1000 genomes]
rs9376504	0.81[EUR][1000 genomes]
rs9385895	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9385896	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9385897	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9385899	0.85[EUR][1000 genomes]
rs9385900	0.85[EUR][1000 genomes]
rs9385901	0.88[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs9385902	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs9385903	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs9385906	0.83[EUR][1000 genomes]
rs9389733	0.95[CEU][hapmap]
rs9389741	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389743	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389744	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389745	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9389746	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9389748	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389749	0.85[EUR][1000 genomes]
rs9389750	0.84[EUR][1000 genomes]
rs9389751	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9389753	0.82[EUR][1000 genomes]
rs9389755	0.85[EUR][1000 genomes]
rs9389757	0.85[EUR][1000 genomes]
rs9389760	0.84[EUR][1000 genomes]
rs9389763	0.82[EUR][1000 genomes]
rs9389767	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9389768	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs9389772	0.81[EUR][1000 genomes]
rs9389773	0.81[EUR][1000 genomes]
rs9399298	0.95[CEU][hapmap]
rs9399303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399304	0.95[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399305	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9399306	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9399307	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9399308	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs9399310	0.82[EUR][1000 genomes]
rs9403134	0.95[CEU][hapmap]
rs9403135	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9403138	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403143	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403145	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9403146	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9403147	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9403148	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs9403149	0.85[EUR][1000 genomes]
rs9403150	0.84[EUR][1000 genomes]
rs9403151	0.84[EUR][1000 genomes]
rs9403153	0.84[EUR][1000 genomes]
rs9403155	0.82[EUR][1000 genomes]
rs9403156	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9403157	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9403159	0.82[EUR][1000 genomes]
rs9403171	0.88[AFR][1000 genomes]
rs9484347	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140369400-140374600	Enhancers	Hela-S3	cervix
2	chr6:140370600-140374800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:140370600-140375400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr6:140370800-140374800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:140370800-140375000	Enhancers	NH-A	brain
6	chr6:140371200-140374600	Enhancers	Fetal Brain Male	brain
7	chr6:140371200-140374600	Enhancers	Osteobl	bone
8	chr6:140371400-140374800	Enhancers	HMEC	breast
9	chr6:140371400-140374800	Enhancers	NHEK	skin
10	chr6:140371400-140374800	Enhancers	NHLF	lung
11	chr6:140371400-140375000	Enhancers	NHDF-Ad	bronchial
12	chr6:140371600-140374600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:140371600-140375400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:140371600-140379400	Weak transcription	Placenta	Placenta
15	chr6:140372200-140375200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:140372400-140375000	Enhancers	Brain Germinal Matrix	brain
17	chr6:140372800-140374400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:140372800-140375000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:140373000-140374800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:140373000-140375000	Enhancers	Fetal Intestine Small	intestine
21	chr6:140373200-140374800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:140373600-140375200	Enhancers	Liver	Liver
23	chr6:140373600-140381000	Weak transcription	HSMM	muscle
24	chr6:140373600-140384200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr6:140373800-140374600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:140373800-140378000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:140374000-140374600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:140374000-140375000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:140374000-140380000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:140374200-140374600	Enhancers	A549	lung
31	chr6:140374200-140374800	Enhancers	Fetal Intestine Large	intestine
32	chr6:140374200-140383800	Weak transcription	Fetal Brain Female	brain

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