Variant report

Variant	rs6902608
Chromosome Location	chr6:163877757-163877758
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	chr6:163870026..163872453-chr6:163876589..163878532,2	K562	blood:
2	chr6:163863925..163866633-chr6:163876893..163879204,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10080505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11964059	0.82[MEX][hapmap]
rs12523713	0.92[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12523978	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17176494	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4112651	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60332904	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6455905	0.92[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6901592	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906081	0.90[EUR][1000 genomes]
rs6906275	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6906725	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6910323	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6914093	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6917030	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6928869	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6936927	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937072	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937097	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73013516	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73013528	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73013553	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73015316	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7748261	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7759606	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761090	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7770852	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9456868	0.91[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458821	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9458823	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458825	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458830	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458837	0.92[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458846	0.90[GIH][hapmap]
rs9458849	0.92[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458854	0.90[GIH][hapmap]
rs9458855	0.90[GIH][hapmap]
rs9458857	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458859	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9654569	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv523664	chr6:163858237-163907885	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6902608	TMPRSS3	trans	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
2	chr6:163845400-163877800	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:163848800-163878400	Weak transcription	Pancreas	Pancrea
4	chr6:163852000-163880000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:163859600-163878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:163860200-163877800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:163860800-163878400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:163860800-163880000	Weak transcription	Lung	lung
9	chr6:163862600-163878000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:163862800-163878600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:163863000-163880200	Weak transcription	Esophagus	oesophagus
12	chr6:163863200-163879200	Weak transcription	Fetal Brain Male	brain
13	chr6:163863600-163878400	Weak transcription	Primary T cells from cord blood	blood
14	chr6:163863600-163878800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:163863800-163877800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:163863800-163877800	Weak transcription	Placenta	Placenta
17	chr6:163863800-163878000	Weak transcription	HMEC	breast
18	chr6:163863800-163878200	Weak transcription	NHEK	skin
19	chr6:163863800-163878800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:163865200-163881400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:163865400-163877800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:163865400-163877800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:163865400-163878600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:163865400-163878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:163865600-163878000	Weak transcription	Fetal Kidney	kidney
26	chr6:163869800-163878600	Weak transcription	Ovary	ovary
27	chr6:163870800-163878000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:163872000-163878800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr6:163872200-163878400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:163872200-163880000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:163872400-163878400	Weak transcription	Gastric	stomach
32	chr6:163872800-163877800	Weak transcription	Small Intestine	intestine
33	chr6:163872800-163878400	Weak transcription	Aorta	Aorta
34	chr6:163873000-163880400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:163873400-163880200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:163873600-163878800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:163874000-163877800	Weak transcription	Left Ventricle	heart
38	chr6:163874400-163880200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:163875000-163878600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:163875000-163880200	Weak transcription	Thymus	Thymus
41	chr6:163875200-163880000	Weak transcription	Fetal Thymus	thymus
42	chr6:163875600-163877800	Weak transcription	Liver	Liver
43	chr6:163875600-163877800	Enhancers	Fetal Heart	heart
44	chr6:163875600-163878400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:163875600-163879200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:163875600-163880000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:163875600-163880400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:163875800-163877800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:163875800-163877800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:163875800-163877800	Enhancers	Brain Cingulate Gyrus	brain

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