Variant report

Variant	rs11590658
Chromosome Location	chr1:224642854-224642855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224619496..224626224-chr1:224640836..224649586,12	K562	blood:
2	chr1:224640725..224643210-chr1:224646698..224648571,2	K562	blood:
3	chr1:224642182..224643861-chr1:225117106..225119317,2	MCF-7	breast:
4	chr1:224641326..224643104-chr1:224643904..224646218,2	MCF-7	breast:
5	chr1:224615678..224629188-chr1:224635437..224647951,56	MCF-7	breast:
6	chr1:224637202..224641034-chr1:224641889..224644811,3	K562	blood:
7	chr1:224617260..224625232-chr1:224640385..224647515,27	MCF-7	breast:
8	chr1:224636445..224639746-chr1:224642433..224645284,3	K562	blood:
9	chr1:224613670..224615210-chr1:224641405..224643090,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162923	Chromatin interaction
ENSG00000143786	Chromatin interaction
ENSG00000185842	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10127813	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10127953	0.86[EUR][1000 genomes]
rs10128058	0.86[EUR][1000 genomes]
rs10159333	0.96[EUR][1000 genomes]
rs10495219	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10753465	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10753466	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10753467	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10753468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs10799569	0.86[EUR][1000 genomes]
rs10916606	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10916607	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10916614	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10916616	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10916617	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10916619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576835	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11577170	0.99[EUR][1000 genomes]
rs11577183	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11578709	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11579952	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs11584057	0.87[EUR][1000 genomes]
rs11584247	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11584980	0.94[CEU][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11586729	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11588973	0.99[EUR][1000 genomes]
rs11800613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs11801436	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11803414	0.94[CEU][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11803981	0.86[EUR][1000 genomes]
rs11805973	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11807763	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11807942	0.85[EUR][1000 genomes]
rs11811053	0.82[EUR][1000 genomes]
rs12062871	0.98[EUR][1000 genomes]
rs12731035	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12731630	0.99[EUR][1000 genomes]
rs12738799	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12739486	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12740255	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12742821	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12742989	0.96[EUR][1000 genomes]
rs12743200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs12745610	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12747286	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12751161	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12754832	0.94[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12755338	0.96[EUR][1000 genomes]
rs12755816	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12758302	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12758579	0.99[EUR][1000 genomes]
rs12759275	0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1539207	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1544196	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16848365	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17503938	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17570292	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2185684	0.99[EUR][1000 genomes]
rs28434172	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2897048	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34791963	0.82[EUR][1000 genomes]
rs35011635	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35031726	0.86[EUR][1000 genomes]
rs35067427	0.99[EUR][1000 genomes]
rs35169600	0.84[EUR][1000 genomes]
rs35277713	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35303987	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35341841	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35365551	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35571080	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35767322	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35804313	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35915186	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35972228	0.82[EUR][1000 genomes]
rs36138926	0.86[EUR][1000 genomes]
rs4653585	1.00[CEU][hapmap]
rs4653587	0.96[EUR][1000 genomes]
rs4654037	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs55730749	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223447	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6426121	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6426123	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6426125	0.96[EUR][1000 genomes]
rs6426126	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs66467176	0.99[EUR][1000 genomes]
rs6663522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs6671751	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs6672859	0.86[EUR][1000 genomes]
rs6675858	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6691779	0.94[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6693287	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6698343	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6701145	1.00[CEU][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67065875	0.86[EUR][1000 genomes]
rs68037178	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71644786	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7365151	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512431	0.86[EUR][1000 genomes]
rs7513208	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7514284	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7514575	0.94[EUR][1000 genomes]
rs7517754	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs7518109	0.86[EUR][1000 genomes]
rs7519734	0.86[EUR][1000 genomes]
rs7522956	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7527044	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7529067	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs7529310	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs867362	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs885606	0.99[EUR][1000 genomes]
rs9970697	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv1013149	chr1:224605943-224646382	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv535312	chr1:224605943-224646382	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11590658	CNIH4	cis	Thyroid	GTEx
rs11590658	CNIH4	cis	Heart Left Ventricle	GTEx
rs11590658	CNIH4	cis	Esophagus Muscularis	GTEx
rs11590658	CNIH4	cis	Muscle Skeletal	GTEx
rs11590658	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224623200-224644400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:224623400-224643000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:224623400-224644600	Weak transcription	Right Ventricle	heart
4	chr1:224623600-224644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:224623600-224644600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:224623800-224644400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:224624000-224644000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:224624000-224644600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:224624000-224644600	Weak transcription	Brain Angular Gyrus	brain
10	chr1:224624000-224645000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:224624000-224645000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:224624000-224645000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:224624000-224646800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:224624800-224644000	Weak transcription	Pancreas	Pancrea
15	chr1:224624800-224644400	Weak transcription	A549	lung
16	chr1:224624800-224645000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:224625200-224644600	Weak transcription	GM12878-XiMat	blood
18	chr1:224625200-224645000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:224627000-224644000	Weak transcription	Placenta	Placenta
20	chr1:224627200-224644400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:224628200-224645000	Weak transcription	Thymus	Thymus
22	chr1:224628400-224644600	Weak transcription	Fetal Lung	lung
23	chr1:224628400-224644800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:224628400-224648800	Weak transcription	Fetal Brain Female	brain
25	chr1:224628600-224644200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:224628600-224653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:224628800-224643800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:224629200-224644200	Weak transcription	Brain Germinal Matrix	brain
29	chr1:224629200-224644600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:224630800-224643000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:224630800-224644600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr1:224631000-224644200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:224631200-224644400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:224635200-224643800	Weak transcription	Lung	lung
35	chr1:224635200-224644000	Weak transcription	Ovary	ovary
36	chr1:224635200-224644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:224635200-224644400	Weak transcription	Left Ventricle	heart
38	chr1:224635200-224644600	Weak transcription	Aorta	Aorta
39	chr1:224635400-224644200	Weak transcription	Adipose Nuclei	Adipose
40	chr1:224635400-224644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:224635400-224644400	Weak transcription	HSMMtube	muscle
42	chr1:224635400-224644400	Weak transcription	NHLF	lung
43	chr1:224635400-224644600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:224635600-224644400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:224635600-224644400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:224635600-224644400	Weak transcription	HSMM	muscle
47	chr1:224635600-224644400	Weak transcription	NHDF-Ad	bronchial
48	chr1:224635600-224644600	Weak transcription	NH-A	brain
49	chr1:224635800-224644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:224635800-224644400	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links