Variant report

Variant	rs3171
Chromosome Location	chr1:93617477-93617478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93615023..93617502-chr1:93621037..93623418,2	K562	blood:
2	chr1:93615373..93618424-chr1:93643538..93645744,3	K562	blood:
3	chr1:93610795..93612747-chr1:93615451..93618016,2	K562	blood:
4	chr1:93606473..93608492-chr1:93616933..93619902,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122483	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1054165	0.82[ASN][1000 genomes]
rs1057256	1.00[ASN][1000 genomes]
rs11164911	1.00[JPT][hapmap]
rs11799928	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800760	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11801175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11801977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11802420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11802822	0.82[ASN][1000 genomes]
rs11805267	0.82[ASN][1000 genomes]
rs11807404	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11808445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1932313	0.82[ASN][1000 genomes]
rs2619816	1.00[CHB][hapmap]
rs2785596	1.00[CHB][hapmap]
rs2815413	1.00[JPT][hapmap]
rs41286833	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41292127	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41298525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41528947	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4847409	1.00[JPT][hapmap]
rs522999	1.00[JPT][hapmap]
rs556888	1.00[JPT][hapmap]
rs55738503	0.82[ASN][1000 genomes]
rs55741554	0.82[ASN][1000 genomes]
rs56657492	0.82[ASN][1000 genomes]
rs571212	1.00[JPT][hapmap]
rs573056	1.00[JPT][hapmap]
rs581825	1.00[JPT][hapmap]
rs58770710	0.82[ASN][1000 genomes]
rs58807475	0.82[ASN][1000 genomes]
rs59368083	0.82[ASN][1000 genomes]
rs59609847	0.82[ASN][1000 genomes]
rs59774396	0.82[ASN][1000 genomes]
rs60079850	0.82[ASN][1000 genomes]
rs60497651	1.00[ASN][1000 genomes]
rs60813039	1.00[ASN][1000 genomes]
rs60868033	0.82[ASN][1000 genomes]
rs61252284	0.82[ASN][1000 genomes]
rs61335636	0.82[ASN][1000 genomes]
rs61690932	0.82[ASN][1000 genomes]
rs628714	1.00[JPT][hapmap]
rs637198	1.00[JPT][hapmap]
rs6541348	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs658877	1.00[JPT][hapmap]
rs6663752	1.00[ASN][1000 genomes]
rs6664190	1.00[ASN][1000 genomes]
rs6667540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6671070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6677862	0.82[ASN][1000 genomes]
rs6679304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6688199	1.00[ASN][1000 genomes]
rs6688513	0.82[ASN][1000 genomes]
rs668944	1.00[JPT][hapmap]
rs6689867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6691556	0.82[ASN][1000 genomes]
rs6704067	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72955374	0.82[ASN][1000 genomes]
rs72955379	0.82[ASN][1000 genomes]
rs72955402	1.00[ASN][1000 genomes]
rs72957210	0.82[ASN][1000 genomes]
rs72957220	0.82[ASN][1000 genomes]
rs72957300	0.82[ASN][1000 genomes]
rs72959204	0.82[ASN][1000 genomes]
rs74101439	0.82[ASN][1000 genomes]
rs74101458	0.82[ASN][1000 genomes]
rs7518171	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7519163	1.00[JPT][hapmap]
rs7529230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7545358	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9324347	0.82[ASN][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
2	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
4	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:93582400-93620400	Weak transcription	Small Intestine	intestine
8	chr1:93582400-93642800	Weak transcription	Gastric	stomach
9	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:93583600-93623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
12	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
13	chr1:93586200-93623400	Weak transcription	Fetal Brain Male	brain
14	chr1:93586800-93621000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:93597400-93625400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
18	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
19	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:93602600-93620400	Weak transcription	Fetal Stomach	stomach
21	chr1:93602600-93620600	Weak transcription	Colonic Mucosa	Colon
22	chr1:93602600-93620600	Weak transcription	Fetal Intestine Small	intestine
23	chr1:93602600-93624200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:93602600-93628800	Weak transcription	Aorta	Aorta
25	chr1:93602600-93630200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:93602600-93630200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:93603400-93620800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:93603400-93624600	Weak transcription	Brain Substantia Nigra	brain
29	chr1:93603600-93620000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:93603600-93620600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:93603600-93621800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:93603600-93629200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:93603800-93620000	Weak transcription	Fetal Lung	lung
34	chr1:93604400-93618400	Weak transcription	HepG2	liver
35	chr1:93604600-93620600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:93606800-93621800	Weak transcription	Brain Germinal Matrix	brain
38	chr1:93606800-93623600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:93606800-93635400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:93608800-93617800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:93609000-93627400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:93611200-93626200	Strong transcription	Fetal Thymus	thymus
43	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:93612600-93620200	Strong transcription	Dnd41	blood
45	chr1:93612800-93619600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:93613000-93626000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:93613000-93626000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:93613200-93625000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:93613200-93626200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:93613200-93627800	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links