Variant report

Variant	rs6769604
Chromosome Location	chr3:113185064-113185065
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	chr3:113184639..113186627-chr3:113186960..113188718,2	MCF-7	breast:
2	chr3:113184124..113185846-chr3:113185911..113187476,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1082588	0.83[AMR][1000 genomes]
rs11537650	0.90[EUR][1000 genomes]
rs12330209	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs13082603	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs13092925	0.91[EUR][1000 genomes]
rs1463643	0.92[EUR][1000 genomes]
rs1471883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1471884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1552433	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16861103	0.95[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs2087130	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2270782	0.95[CEU][hapmap];0.82[AMR][1000 genomes]
rs2270783	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs2270785	0.90[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs2291905	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs2399477	0.95[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs2399480	0.90[EUR][1000 genomes]
rs2669909	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2936812	0.83[JPT][hapmap]
rs4396864	0.94[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes]
rs60634072	0.86[EUR][1000 genomes]
rs6438160	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6783387	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6793704	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6805535	0.90[CEU][hapmap]
rs712530	0.95[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs72946748	0.87[EUR][1000 genomes]
rs7618226	0.89[EUR][1000 genomes]
rs7623919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7628945	0.92[EUR][1000 genomes]
rs7631335	0.92[EUR][1000 genomes]
rs7635676	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637618	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7646188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7650671	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775214	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs775215	0.95[CEU][hapmap]
rs775217	0.83[AMR][1000 genomes]
rs808949	0.95[CEU][hapmap];0.83[AMR][1000 genomes]
rs808950	0.95[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs810209	0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs9842559	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9846539	0.90[EUR][1000 genomes]
rs9852703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9854686	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870996	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9874747	0.88[EUR][1000 genomes]
rs9877649	0.90[EUR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6769604	BOC	cis	parietal	SCAN
rs6769604	BOC	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113146000-113191000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:113160200-113190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:113160400-113186800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:113160400-113188800	Weak transcription	Colonic Mucosa	Colon
5	chr3:113160400-113191200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:113160400-113192800	Weak transcription	Stomach Mucosa	stomach
7	chr3:113160600-113188600	Weak transcription	Psoas Muscle	Psoas
8	chr3:113160600-113190600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:113160600-113203800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:113160800-113187000	Weak transcription	HUVEC	blood vessel
11	chr3:113160800-113187600	Weak transcription	NHLF	lung
12	chr3:113160800-113189400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:113160800-113189400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:113160800-113189600	Weak transcription	NHEK	skin
15	chr3:113160800-113203800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:113160800-113203800	Weak transcription	Aorta	Aorta
17	chr3:113160800-113224800	Weak transcription	Placenta	Placenta
18	chr3:113160800-113232600	Weak transcription	Right Ventricle	heart
19	chr3:113161000-113189600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:113161000-113189600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:113161000-113190800	Weak transcription	K562	blood
22	chr3:113161400-113192200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:113164000-113185600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:113166200-113188800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:113166600-113186400	Weak transcription	A549	lung
26	chr3:113166600-113203800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:113169000-113186600	Weak transcription	Small Intestine	intestine
28	chr3:113169800-113191600	Weak transcription	Fetal Brain Male	brain
29	chr3:113172600-113187000	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:113172600-113203800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:113172800-113232800	Weak transcription	HSMMtube	muscle
32	chr3:113173200-113187000	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:113173800-113190200	Weak transcription	Fetal Heart	heart
34	chr3:113174600-113190200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:113175000-113190600	Weak transcription	Brain Germinal Matrix	brain
36	chr3:113176200-113186600	Weak transcription	Osteobl	bone
37	chr3:113176400-113233200	Weak transcription	Gastric	stomach
38	chr3:113177000-113186200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:113177400-113225800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:113177600-113224400	Weak transcription	Spleen	Spleen
41	chr3:113177800-113187000	Weak transcription	Lung	lung
42	chr3:113179400-113186400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:113179400-113186800	Weak transcription	GM12878-XiMat	blood
44	chr3:113179400-113187400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:113179600-113186200	Weak transcription	HepG2	liver
46	chr3:113179600-113186400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:113179600-113186400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:113179600-113186400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:113179600-113186600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:113179600-113186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links