Variant report

Variant	rs11584057
Chromosome Location	chr1:224685350-224685351
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224683423..224687942-chr1:224688283..224691740,8	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10127813	0.95[CEU][hapmap]
rs10159333	0.85[EUR][1000 genomes]
rs10495219	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10753465	0.95[CEU][hapmap]
rs10753466	0.95[CEU][hapmap]
rs10753467	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10753468	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs10916606	0.95[CEU][hapmap]
rs10916607	0.95[CEU][hapmap]
rs10916614	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs10916616	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10916617	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10916619	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs11576835	0.95[CEU][hapmap]
rs11577170	0.88[EUR][1000 genomes]
rs11578709	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579952	0.91[CEU][hapmap]
rs11584638	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11584980	0.90[CEU][hapmap]
rs11586729	0.95[CEU][hapmap]
rs11588973	0.87[EUR][1000 genomes]
rs11590658	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs11800613	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs11801436	0.95[CEU][hapmap]
rs11801645	0.95[CEU][hapmap]
rs11803414	0.90[CEU][hapmap]
rs11805973	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs11807763	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs12062871	0.89[EUR][1000 genomes]
rs12731630	0.88[EUR][1000 genomes]
rs12738799	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12739486	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12740255	0.90[CEU][hapmap]
rs12742989	0.84[EUR][1000 genomes]
rs12743200	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs12745610	0.95[CEU][hapmap]
rs12747286	0.81[EUR][1000 genomes]
rs12751161	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12754832	0.94[CEU][hapmap]
rs12755338	0.84[EUR][1000 genomes]
rs12755816	0.95[CEU][hapmap]
rs12758579	0.88[EUR][1000 genomes]
rs1539207	0.95[CEU][hapmap]
rs1544196	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs16848365	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs17503938	0.90[CEU][hapmap]
rs17570292	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185684	0.88[EUR][1000 genomes]
rs28434172	0.81[EUR][1000 genomes]
rs2897048	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs34791963	0.81[EUR][1000 genomes]
rs35011635	0.83[EUR][1000 genomes]
rs35067427	0.88[EUR][1000 genomes]
rs35277713	0.84[EUR][1000 genomes]
rs35303987	0.84[EUR][1000 genomes]
rs35365551	0.80[EUR][1000 genomes]
rs35571080	0.87[EUR][1000 genomes]
rs35804313	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35915186	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653585	0.95[CEU][hapmap]
rs4653587	0.85[EUR][1000 genomes]
rs4654037	0.95[CEU][hapmap]
rs55730749	0.87[EUR][1000 genomes]
rs6426121	0.95[CEU][hapmap]
rs6426123	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6426125	0.85[EUR][1000 genomes]
rs6426126	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs66467176	0.87[EUR][1000 genomes]
rs66530931	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6663522	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs6671751	0.91[CEU][hapmap]
rs6675858	0.90[CEU][hapmap]
rs6678608	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6691779	0.90[CEU][hapmap]
rs6693287	0.95[CEU][hapmap]
rs6698343	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701145	0.95[CEU][hapmap]
rs71644786	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7365151	0.87[EUR][1000 genomes]
rs7513208	0.91[CEU][hapmap]
rs7514284	0.86[CEU][hapmap]
rs7514575	0.84[EUR][1000 genomes]
rs7517754	0.86[CEU][hapmap]
rs7522956	0.95[CEU][hapmap]
rs7527044	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7529067	0.91[CEU][hapmap]
rs7529310	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs867362	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs885606	0.88[EUR][1000 genomes]
rs9970697	0.86[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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11584057	CNIH4	cis	Thyroid	GTEx
rs11584057	CNIH4	cis	Muscle Skeletal	GTEx
rs11584057	CNIH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224677800-224685400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:224679800-224689600	Weak transcription	Pancreas	Pancrea
3	chr1:224680000-224685600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:224681600-224685400	Weak transcription	Esophagus	oesophagus
5	chr1:224681800-224685600	Weak transcription	Stomach Mucosa	stomach
6	chr1:224682200-224685400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:224682200-224685800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:224682800-224686200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:224682800-224690200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:224683200-224685400	Weak transcription	Right Atrium	heart
11	chr1:224683200-224685600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:224683200-224686000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:224684200-224685400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:224684200-224685400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:224684200-224685400	Weak transcription	HSMMtube	muscle
16	chr1:224684200-224685800	Weak transcription	Liver	Liver
17	chr1:224684200-224685800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:224684200-224685800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:224684400-224685800	Weak transcription	Gastric	stomach
20	chr1:224684600-224687200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:224684800-224685400	Enhancers	HUVEC	blood vessel
22	chr1:224684800-224685400	Enhancers	Osteobl	bone
23	chr1:224684800-224685600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:224684800-224685600	Enhancers	Dnd41	blood
25	chr1:224684800-224685800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:224684800-224686200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:224684800-224686200	Enhancers	NHDF-Ad	bronchial
28	chr1:224684800-224686800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr1:224685000-224685400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:224685000-224685600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:224685000-224685800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:224685000-224685800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:224685000-224686200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:224685000-224686200	Enhancers	NHLF	lung
35	chr1:224685200-224685400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:224685200-224685400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr1:224685200-224685400	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:224685200-224685400	Enhancers	K562	blood
39	chr1:224685200-224685400	Enhancers	NHEK	skin
40	chr1:224685200-224685600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr1:224685200-224685600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:224685200-224685800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:224685200-224685800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:224685200-224685800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr1:224685200-224685800	Enhancers	Adipose Nuclei	Adipose
46	chr1:224685200-224685800	Enhancers	Hela-S3	cervix
47	chr1:224685200-224685800	Enhancers	HMEC	breast
48	chr1:224685200-224685800	Enhancers	NH-A	brain
49	chr1:224685200-224686000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr1:224685200-224686000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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