Variant report

Variant	rs12949267
Chromosome Location	chr17:67318946-67318947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1011549	0.83[ASN][1000 genomes]
rs10512526	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10512527	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11077445	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs112914	1.00[JPT][hapmap]
rs11649744	0.84[ASN][1000 genomes]
rs11650658	0.85[ASN][1000 genomes]
rs11650955	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs11652207	0.82[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11654323	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs11656389	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11656456	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12449649	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12450167	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12450522	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs12450743	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12452340	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12937947	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12938064	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12938097	0.81[ASN][1000 genomes]
rs12940364	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12941297	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12942867	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12943504	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12944980	0.83[ASN][1000 genomes]
rs12945481	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12946776	0.83[ASN][1000 genomes]
rs1468513	0.96[CEU][hapmap]
rs1550828	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs1558168	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs15886	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1990248	0.83[EUR][1000 genomes]
rs2441358	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34985085	0.84[ASN][1000 genomes]
rs4310935	0.84[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4310936	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs471193	0.95[JPT][hapmap]
rs475283	0.95[JPT][hapmap]
rs476677	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481876	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs486840	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs488714	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494946	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs523505	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs531586	0.94[JPT][hapmap]
rs534645	1.00[JPT][hapmap]
rs544940	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs557491	0.85[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs568536	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6501313	1.00[JPT][hapmap]
rs7213377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223895	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7225762	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs817121	1.00[JPT][hapmap]
rs817126	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs817127	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9302893	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
3	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv575935	chr17:67256162-67327806	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
6	nsv457890	chr17:67264339-67327806	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
7	nsv575936	chr17:67264339-67327806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
8	nsv908706	chr17:67290840-67332355	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
9	nsv575937	chr17:67304447-67327806	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12949267	GH2	cis	cerebellum	SCAN
rs12949267	PRKAR1A	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
2	chr17:67261400-67322000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:67290200-67319600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr17:67291800-67321800	Weak transcription	Esophagus	oesophagus
5	chr17:67297000-67319400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:67297000-67321800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr17:67304200-67321800	Weak transcription	HUVEC	blood vessel
8	chr17:67305200-67321600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:67306000-67321800	Weak transcription	Placenta	Placenta
10	chr17:67306400-67321000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr17:67306600-67319600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:67307000-67321800	Weak transcription	Left Ventricle	heart
13	chr17:67307000-67321800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:67307200-67319000	Weak transcription	Fetal Intestine Large	intestine
15	chr17:67307200-67321800	Weak transcription	Thymus	Thymus
16	chr17:67308000-67321200	Weak transcription	Fetal Intestine Small	intestine
17	chr17:67310200-67321000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr17:67311000-67322000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr17:67311200-67319000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr17:67311200-67319400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr17:67311200-67320400	Weak transcription	Pancreas	Pancrea
22	chr17:67311200-67320400	Weak transcription	Psoas Muscle	Psoas
23	chr17:67311200-67321800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr17:67311200-67322000	Weak transcription	Brain Anterior Caudate	brain
25	chr17:67311400-67319200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:67313800-67319200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr17:67314000-67320400	Weak transcription	HMEC	breast
28	chr17:67314000-67321600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr17:67314200-67321600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:67315800-67321400	Weak transcription	Liver	Liver
31	chr17:67316200-67320400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:67316400-67321800	Weak transcription	Osteobl	bone
33	chr17:67316800-67321800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:67317000-67320000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr17:67317000-67321600	Weak transcription	NHDF-Ad	bronchial
36	chr17:67317400-67319400	Weak transcription	GM12878-XiMat	blood
37	chr17:67317600-67319800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:67317800-67319000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr17:67317800-67319000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr17:67317800-67319000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr17:67318600-67319800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr17:67318600-67320000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr17:67318600-67320200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr17:67318600-67320400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr17:67318800-67319200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr17:67318800-67319400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr17:67318800-67319600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr17:67318800-67321400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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