Variant report

Variant	rs12347811
Chromosome Location	chr9:3401990-3401991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10115757	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[YRI][hapmap]
rs10115791	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs10117357	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10117431	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10117846	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs10124292	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10124295	0.91[CEU][hapmap]
rs10814038	0.90[CHB][hapmap]
rs10814039	0.91[CHB][hapmap]
rs10814096	0.82[CHB][hapmap]
rs10971661	1.00[CHB][hapmap]
rs10971665	0.90[CHB][hapmap]
rs10971685	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10971806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10972042	0.82[CHB][hapmap]
rs10972079	0.80[CEU][hapmap]
rs11536748	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12002215	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12335763	0.91[CHB][hapmap]
rs12337095	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs12338587	0.96[EUR][1000 genomes]
rs12338927	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12339955	0.82[CHB][hapmap]
rs12340535	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12341652	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[EUR][1000 genomes]
rs12341737	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12343385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12346432	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[EUR][1000 genomes]
rs12347985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12554323	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs13286511	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13290412	0.89[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs13295925	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs13297034	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs13298219	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs13298908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13300358	0.80[CEU][hapmap]
rs13302664	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13302841	0.80[CEU][hapmap]
rs1348369	1.00[CHB][hapmap]
rs16924266	0.90[CEU][hapmap]
rs1998976	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs34065256	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34233417	0.94[EUR][1000 genomes]
rs34331766	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35545940	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35824006	0.84[EUR][1000 genomes]
rs35945655	0.84[EUR][1000 genomes]
rs3758195	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758196	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4237147	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs4741825	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4741826	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4741829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57004251	0.80[EUR][1000 genomes]
rs60796901	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6476436	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs6476451	0.80[EUR][1000 genomes]
rs66463406	0.88[EUR][1000 genomes]
rs66763574	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7022711	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs7024933	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7028812	0.90[CEU][hapmap]
rs7040113	0.91[CEU][hapmap];0.84[YRI][hapmap]
rs7041836	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7043493	0.91[CEU][hapmap]
rs71506638	0.84[EUR][1000 genomes]
rs71506639	0.96[EUR][1000 genomes]
rs7864440	0.82[CHB][hapmap]
rs7875889	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs9695619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv613147	chr9:3368111-3440355	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1849738	chr9:3389223-3404434	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
12	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
2	chr9:3382200-3425000	Weak transcription	Aorta	Aorta
3	chr9:3383200-3410000	Weak transcription	Fetal Brain Male	brain
4	chr9:3386200-3409600	Weak transcription	Psoas Muscle	Psoas
5	chr9:3387200-3433800	Weak transcription	Pancreas	Pancrea
6	chr9:3398800-3403200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:3398800-3415400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:3398800-3418600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:3398800-3423400	Weak transcription	Primary T cells from cord blood	blood
10	chr9:3398800-3437200	Weak transcription	Primary B cells from cord blood	blood
11	chr9:3400800-3402400	Enhancers	Fetal Brain Female	brain
12	chr9:3401000-3402000	Enhancers	Fetal Lung	lung
13	chr9:3401000-3402600	Enhancers	Brain Germinal Matrix	brain
14	chr9:3401000-3403800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr9:3401000-3404000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr9:3401200-3402000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:3401200-3402400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr9:3401200-3402600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr9:3401400-3402000	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr9:3401400-3402000	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr9:3401400-3402000	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr9:3401400-3402200	Enhancers	Brain Cingulate Gyrus	brain
23	chr9:3401400-3402200	Enhancers	HMEC	breast
24	chr9:3401400-3402400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:3401400-3402400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr9:3401400-3402400	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr9:3401400-3404200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr9:3401400-3408000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:3401600-3402000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr9:3401600-3402000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:3401600-3402000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:3401600-3402000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:3401600-3402000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr9:3401600-3402200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr9:3401600-3402200	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr9:3401600-3402200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:3401600-3402200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:3401600-3402200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:3401600-3402400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:3401800-3402000	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr9:3401800-3402000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr9:3401800-3402000	Enhancers	Duodenum Mucosa	Duodenum
43	chr9:3401800-3402000	Enhancers	Fetal Stomach	stomach
44	chr9:3401800-3402200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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