Variant report

Variant	rs17570292
Chromosome Location	chr1:224681894-224681895
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224677828..224680425-chr1:224681329..224683166,2	K562	blood:
2	chr1:224640045..224642435-chr1:224680202..224683058,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10127813	0.95[CEU][hapmap]
rs10159333	0.86[EUR][1000 genomes]
rs10495219	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10753465	0.95[CEU][hapmap]
rs10753466	0.95[CEU][hapmap]
rs10753467	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10753468	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs10916606	0.95[CEU][hapmap]
rs10916607	0.95[CEU][hapmap]
rs10916614	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10916616	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10916617	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10916619	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11576835	0.95[CEU][hapmap]
rs11577170	0.89[EUR][1000 genomes]
rs11578709	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579952	0.91[CEU][hapmap]
rs11584057	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584638	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11584980	0.90[CEU][hapmap]
rs11586729	0.95[CEU][hapmap]
rs11588973	0.88[EUR][1000 genomes]
rs11590658	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11800613	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs11801436	0.95[CEU][hapmap]
rs11801645	0.95[CEU][hapmap]
rs11803414	0.90[CEU][hapmap]
rs11805973	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11807763	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12062871	0.90[EUR][1000 genomes]
rs12731630	0.89[EUR][1000 genomes]
rs12738799	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12739486	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12740255	0.90[CEU][hapmap]
rs12742989	0.86[EUR][1000 genomes]
rs12743200	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs12745610	0.95[CEU][hapmap]
rs12747286	0.83[EUR][1000 genomes]
rs12751161	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12754832	0.94[CEU][hapmap]
rs12755338	0.85[EUR][1000 genomes]
rs12755816	0.95[CEU][hapmap]
rs12758302	0.81[EUR][1000 genomes]
rs12758579	0.89[EUR][1000 genomes]
rs1539207	0.95[CEU][hapmap]
rs1544196	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs16848365	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs17503938	0.90[CEU][hapmap]
rs2185684	0.89[EUR][1000 genomes]
rs28434172	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2897048	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34791963	0.83[EUR][1000 genomes]
rs35011635	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35067427	0.89[EUR][1000 genomes]
rs35277713	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35303987	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35365551	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35571080	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35767322	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35804313	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35915186	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653585	0.95[CEU][hapmap]
rs4653587	0.86[EUR][1000 genomes]
rs4654037	0.95[CEU][hapmap]
rs55730749	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6426121	0.95[CEU][hapmap]
rs6426123	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6426125	0.86[EUR][1000 genomes]
rs6426126	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs66467176	0.88[EUR][1000 genomes]
rs66530931	0.90[EUR][1000 genomes]
rs6663522	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs6671751	0.91[CEU][hapmap]
rs6675858	0.90[CEU][hapmap]
rs6678608	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6691779	0.90[CEU][hapmap]
rs6693287	0.95[CEU][hapmap]
rs6698343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701145	0.95[CEU][hapmap]
rs71644786	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7365151	0.82[AMR][1000 genomes];0.88[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];0.84[EUR][1000 genomes]
rs7529067	0.91[CEU][hapmap]
rs7529310	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs867362	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs885606	0.89[EUR][1000 genomes]
rs9970697	0.88[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17570292	CNIH4	cis	Thyroid	GTEx
rs17570292	CNIH4	cis	Nerve Tibial	GTEx
rs17570292	CNIH4	cis	Muscle Skeletal	GTEx
rs17570292	CNIH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224677200-224685000	Weak transcription	NHLF	lung
2	chr1:224677600-224682600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:224677600-224683400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:224677800-224683400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:224677800-224684800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:224677800-224684800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:224677800-224685400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:224678000-224683000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:224678200-224683200	Weak transcription	Osteobl	bone
10	chr1:224678800-224682600	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:224679200-224683400	Weak transcription	HSMM	muscle
12	chr1:224679800-224689600	Weak transcription	Pancreas	Pancrea
13	chr1:224680000-224683000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:224680000-224685600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:224680400-224682000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:224680400-224682000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:224680600-224682000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:224680800-224682000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr1:224680800-224682200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:224680800-224683400	Weak transcription	NHDF-Ad	bronchial
21	chr1:224681000-224682200	Enhancers	Fetal Intestine Small	intestine
22	chr1:224681000-224682400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:224681000-224682400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:224681000-224683000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:224681000-224683200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:224681200-224682000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:224681200-224682400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:224681600-224684800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:224681600-224685400	Weak transcription	Esophagus	oesophagus
30	chr1:224681800-224684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:224681800-224685600	Weak transcription	Stomach Mucosa	stomach

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