Variant report

Variant	rs11579952
Chromosome Location	chr1:224547192-224547193
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224545456..224548563-chr1:224564069..224566245,3	K562	blood:
2	chr1:224544599..224546252-chr1:224546494..224549421,2	MCF-7	breast:
3	chr1:224547136..224549294-chr1:224550559..224553232,2	K562	blood:
4	chr1:224544325..224548164-chr1:224620481..224623704,4	K562	blood:
5	chr1:224545747..224547349-chr1:224557974..224560385,2	K562	blood:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction
ENSG00000143771	Chromatin interaction
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10127813	0.95[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127953	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10128058	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10159333	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10495219	0.95[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10753465	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10753466	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10753467	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10753468	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10799569	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916606	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs10916607	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916614	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10916616	0.95[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10916617	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10916619	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11576835	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs11577170	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11577183	0.96[EUR][1000 genomes]
rs11584247	0.96[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11584980	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs11586729	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs11588973	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11590658	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs11800613	0.95[CEU][hapmap];0.97[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11801436	0.95[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11803414	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805973	0.91[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11807763	0.95[CEU][hapmap];0.97[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11807942	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811053	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12062871	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12731035	0.94[EUR][1000 genomes]
rs12731630	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12738799	0.95[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12739486	0.95[CEU][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12740255	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs12742821	0.96[EUR][1000 genomes]
rs12742989	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12743200	0.95[CEU][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12745610	0.95[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12747286	0.90[EUR][1000 genomes]
rs12751161	0.95[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12754832	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs12755338	0.84[EUR][1000 genomes]
rs12755816	0.95[CEU][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12758302	0.83[EUR][1000 genomes]
rs12758579	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12759275	0.96[EUR][1000 genomes]
rs1539207	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1544196	0.95[CEU][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16848365	0.95[CEU][hapmap];0.97[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17503938	0.90[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185684	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28434172	0.88[EUR][1000 genomes]
rs2897048	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs35011635	0.88[EUR][1000 genomes]
rs35031726	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35067427	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35169600	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35277713	0.88[EUR][1000 genomes]
rs35303987	0.88[EUR][1000 genomes]
rs35341841	0.94[EUR][1000 genomes]
rs35365551	0.84[EUR][1000 genomes]
rs35571080	0.86[EUR][1000 genomes]
rs35915186	0.82[EUR][1000 genomes]
rs35972228	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36138926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653585	0.95[CEU][hapmap]
rs4653587	0.89[EUR][1000 genomes]
rs4654037	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55730749	0.86[EUR][1000 genomes]
rs56223447	0.96[EUR][1000 genomes]
rs6426121	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs6426123	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6426125	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6426126	0.95[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66467176	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6663522	0.95[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6671751	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672859	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6675858	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691779	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs6693287	0.95[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6701145	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs67065875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68037178	0.95[EUR][1000 genomes]
rs7365151	0.86[EUR][1000 genomes]
rs7512431	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7513208	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514284	0.86[CEU][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7514575	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7517754	0.95[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518109	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7519734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522956	0.95[CEU][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7527044	0.95[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7529067	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529310	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs867362	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs885606	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9970697	0.85[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	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11579952	CNIH4	cis	Adipose Subcutaneous	GTEx
rs11579952	CNIH4	cis	Muscle Skeletal	GTEx
rs11579952	CNIH4	cis	Esophagus Muscularis	GTEx
rs11579952	CNIH4	cis	Nerve Tibial	GTEx
rs11579952	CNIH4	cis	Stomach	GTEx
rs11579952	CNIH4	cis	Thyroid	GTEx
rs11579952	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs11579952	CNIH4	cis	Esophagus Mucosa	GTEx
rs11579952	CNIH4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545200-224555200	Weak transcription	Spleen	Spleen
2	chr1:224545400-224547400	Weak transcription	Gastric	stomach
3	chr1:224545400-224547800	Enhancers	Pancreas	Pancrea
4	chr1:224545400-224553800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:224545400-224559000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:224545600-224547600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr1:224545600-224555200	Weak transcription	Lung	lung
8	chr1:224545600-224555200	Weak transcription	Ovary	ovary
9	chr1:224545800-224547200	Enhancers	Colon Smooth Muscle	Colon
10	chr1:224545800-224547400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:224545800-224547800	Enhancers	Esophagus	oesophagus
12	chr1:224545800-224549800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:224545800-224555000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:224545800-224562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
16	chr1:224546000-224547200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:224546000-224547200	Enhancers	Fetal Heart	heart
18	chr1:224546000-224547200	Enhancers	Fetal Intestine Large	intestine
19	chr1:224546000-224548000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:224546000-224548000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:224546000-224548400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:224546000-224548600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:224546000-224548600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:224546000-224548600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:224546000-224549800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:224546000-224551600	Weak transcription	Thymus	Thymus
27	chr1:224546000-224554600	Weak transcription	Liver	Liver
28	chr1:224546000-224555200	Weak transcription	Fetal Kidney	kidney
29	chr1:224546000-224556400	Weak transcription	Brain Angular Gyrus	brain
30	chr1:224546000-224563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:224546200-224547200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:224546200-224547200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:224546200-224547200	Weak transcription	Fetal Stomach	stomach
35	chr1:224546200-224547200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:224546200-224547400	Weak transcription	Right Atrium	heart
37	chr1:224546200-224547400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:224546200-224547600	Enhancers	A549	lung
39	chr1:224546200-224547800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:224546200-224548000	Enhancers	Fetal Brain Male	brain
41	chr1:224546200-224548000	Enhancers	HepG2	liver
42	chr1:224546200-224548600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:224546200-224548600	Enhancers	Primary T cells from cord blood	blood
44	chr1:224546200-224549400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:224546200-224550800	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:224546200-224551000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr1:224546200-224551200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:224546200-224551400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:224546200-224551400	Weak transcription	HSMMtube	muscle
50	chr1:224546200-224551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links