Variant report

Variant	rs9847479
Chromosome Location	chr3:51211096-51211097
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10212250	0.91[CEU][hapmap]
rs10446473	0.82[EUR][1000 genomes]
rs11130274	0.91[CEU][hapmap]
rs11130280	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130282	0.91[CEU][hapmap]
rs11130283	0.84[EUR][1000 genomes]
rs11130286	1.00[CEU][hapmap]
rs11130290	1.00[CEU][hapmap]
rs11706571	1.00[CEU][hapmap]
rs11711643	0.85[EUR][1000 genomes]
rs13064149	0.84[EUR][1000 genomes]
rs13080170	0.87[ASN][1000 genomes]
rs1318649	1.00[CEU][hapmap]
rs1383252	0.92[CEU][hapmap]
rs1480357	0.91[CEU][hapmap]
rs1480358	0.91[CEU][hapmap]
rs1480360	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1480362	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1480363	0.92[CEU][hapmap]
rs1480364	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1552072	0.91[CEU][hapmap]
rs1552073	0.91[CEU][hapmap]
rs2061950	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2061951	0.92[CEU][hapmap]
rs2170178	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2219891	1.00[CEU][hapmap]
rs2291162	0.84[EUR][1000 genomes]
rs2355941	0.91[CEU][hapmap]
rs2355943	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2355945	0.82[EUR][1000 genomes]
rs28708817	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28810453	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2883809	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35356497	0.87[ASN][1000 genomes]
rs3856932	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4244697	0.91[CEU][hapmap]
rs4301044	0.91[CEU][hapmap]
rs4328835	0.91[CEU][hapmap]
rs4356848	0.89[ASN][1000 genomes]
rs4364203	0.82[ASN][1000 genomes]
rs4367100	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4367101	0.91[CEU][hapmap]
rs4378999	0.92[CEU][hapmap]
rs4434173	0.89[ASN][1000 genomes]
rs4453876	0.91[CEU][hapmap]
rs4475072	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528983	0.92[CEU][hapmap]
rs4532165	0.91[CEU][hapmap]
rs4538365	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4557148	1.00[CEU][hapmap]
rs4560329	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4568177	0.91[CEU][hapmap]
rs4572801	0.88[ASN][1000 genomes]
rs4927969	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927970	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4927973	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974092	1.00[CEU][hapmap]
rs4974094	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4974095	0.91[CEU][hapmap]
rs4974099	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4974108	1.00[CEU][hapmap]
rs4974109	0.91[CEU][hapmap]
rs62257481	0.84[EUR][1000 genomes]
rs62257499	0.82[EUR][1000 genomes]
rs6445455	0.91[CEU][hapmap]
rs6445501	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445549	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445551	0.91[CEU][hapmap]
rs6445601	1.00[CEU][hapmap]
rs6445604	1.00[CEU][hapmap]
rs6445611	1.00[CEU][hapmap]
rs6772197	0.90[ASN][1000 genomes]
rs6772664	0.91[CEU][hapmap]
rs6777719	0.91[CEU][hapmap]
rs6779658	0.91[CEU][hapmap]
rs6783235	0.84[EUR][1000 genomes]
rs6784455	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787805	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796642	0.83[ASN][1000 genomes]
rs6796847	1.00[CEU][hapmap]
rs6799722	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6809080	0.89[CEU][hapmap]
rs7427006	0.92[CEU][hapmap]
rs7614317	1.00[CEU][hapmap]
rs7616967	0.81[EUR][1000 genomes]
rs7618173	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7619584	0.92[CEU][hapmap]
rs7628533	0.91[CEU][hapmap]
rs7630714	1.00[CEU][hapmap]
rs7630730	0.91[CEU][hapmap]
rs7634799	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7640083	1.00[CEU][hapmap]
rs7644957	0.91[CEU][hapmap]
rs7649069	0.91[CEU][hapmap]
rs7651141	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs899750	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs922612	0.91[CEU][hapmap]
rs9815781	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9832672	1.00[CEU][hapmap]
rs9836464	0.81[EUR][1000 genomes]
rs9839484	0.87[ASN][1000 genomes]
rs9844581	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9855442	0.92[CEU][hapmap]
rs9855454	0.82[CEU][hapmap]
rs9856566	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9857598	0.84[EUR][1000 genomes]
rs9858412	0.91[CEU][hapmap]
rs9860403	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9865532	0.89[ASN][1000 genomes]
rs9869123	0.89[CEU][hapmap]
rs9871539	0.91[CEU][hapmap]
rs9877188	1.00[CEU][hapmap]
rs9878100	0.91[CEU][hapmap]
rs9883739	0.92[CEU][hapmap]
rs995543	1.00[CEU][hapmap];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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9847479	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51209600-51213200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
2	chr3:51209800-51211600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr3:51209800-51211600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
4	chr3:51209800-51212400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
5	chr3:51209800-51212800	ZNF genes & repeats	Fetal Brain Female	brain
6	chr3:51210000-51211400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
7	chr3:51210000-51212400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
8	chr3:51210000-51213000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:51210400-51211600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:51210400-51213600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:51210600-51211200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:51210600-51211200	ZNF genes & repeats	Brain Hippocampus Middle	brain
13	chr3:51210600-51211400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
14	chr3:51210600-51211400	ZNF genes & repeats	Brain Substantia Nigra	brain
15	chr3:51210600-51211400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
16	chr3:51210600-51211600	ZNF genes & repeats	Brain Angular Gyrus	brain
17	chr3:51210600-51211600	ZNF genes & repeats	Brain Anterior Caudate	brain
18	chr3:51210600-51212600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:51210600-51212800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:51210600-51212800	ZNF genes & repeats	Brain Germinal Matrix	brain
21	chr3:51211000-51212800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:51211000-51215200	Weak transcription	Left Ventricle	heart

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