Variant report

Variant	rs7969887
Chromosome Location	chr12:66717692-66717693
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10748038	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10748039	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784521	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784524	0.94[CEU][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10878403	0.86[CHB][hapmap]
rs11176137	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs11176138	0.87[CEU][hapmap];0.97[EUR][1000 genomes]
rs11176139	0.97[EUR][1000 genomes]
rs11176142	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs11176144	0.91[EUR][1000 genomes]
rs12367438	0.92[EUR][1000 genomes]
rs12816200	0.92[EUR][1000 genomes]
rs1495495	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1898305	0.92[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971302	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118139	0.91[CHB][hapmap]
rs3741603	0.89[CEU][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4382951	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4554930	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581676	0.89[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7132724	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7133479	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7298868	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7315366	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs7316880	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7956960	0.96[EUR][1000 genomes]
rs7957877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959466	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964860	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7973358	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978354	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7969887	HELB	cis	cerebellum	SCAN
rs7969887	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs7969887	HELB	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66696800-66719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:66696800-66723600	Weak transcription	HSMM	muscle
3	chr12:66696800-66734200	Weak transcription	HSMMtube	muscle
4	chr12:66697000-66725000	Weak transcription	Ovary	ovary
5	chr12:66697200-66725600	Weak transcription	Fetal Heart	heart
6	chr12:66697200-66733800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:66697200-66734800	Weak transcription	Esophagus	oesophagus
8	chr12:66697200-66735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:66697200-66742200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:66697400-66719800	Weak transcription	Psoas Muscle	Psoas
11	chr12:66697400-66724800	Weak transcription	Pancreas	Pancrea
12	chr12:66697400-66732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:66697400-66732400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:66697400-66735000	Weak transcription	Right Ventricle	heart
15	chr12:66697800-66725000	Weak transcription	Colonic Mucosa	Colon
16	chr12:66698200-66725200	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:66698200-66735000	Weak transcription	Fetal Brain Female	brain
18	chr12:66698400-66732400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:66698400-66734800	Weak transcription	HepG2	liver
20	chr12:66699000-66735000	Weak transcription	K562	blood
21	chr12:66702400-66724800	Weak transcription	Aorta	Aorta
22	chr12:66702600-66734800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:66704200-66725600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:66704200-66733600	Weak transcription	A549	lung
25	chr12:66704200-66735000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:66704400-66724800	Weak transcription	Lung	lung
27	chr12:66704400-66732200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:66704400-66733600	Weak transcription	Brain Anterior Caudate	brain
29	chr12:66704400-66741800	Weak transcription	Hela-S3	cervix
30	chr12:66704600-66721800	Weak transcription	Fetal Intestine Small	intestine
31	chr12:66704600-66725000	Weak transcription	Spleen	Spleen
32	chr12:66704600-66725200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:66704800-66724600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:66704800-66725000	Weak transcription	Placenta	Placenta
35	chr12:66705000-66729000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:66705200-66720400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:66705200-66724800	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:66705200-66724800	Weak transcription	Gastric	stomach
39	chr12:66705200-66730200	Weak transcription	Left Ventricle	heart
40	chr12:66705200-66731800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:66705400-66725200	Weak transcription	Brain Germinal Matrix	brain
42	chr12:66705800-66724800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:66705800-66732400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:66705800-66732600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:66705800-66734800	Weak transcription	Fetal Stomach	stomach
46	chr12:66706200-66732600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:66706400-66723600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:66708200-66724800	Weak transcription	Small Intestine	intestine
49	chr12:66708200-66732400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:66709000-66720800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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