Variant report

Variant	rs7804020
Chromosome Location	chr7:102795951-102795952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr7:102795877-102796524	GM12878	blood:	n/a	chr7:102796238-102796253 chr7:102796256-102796271
2	EBF1	chr7:102795744-102796474	GM12878	blood:	n/a	chr7:102795999-102796010
3	IRF4	chr7:102795912-102796413	GM12878	blood:	n/a	n/a
4	ZNF384	chr7:102795652-102796054	GM12878	blood:	n/a	n/a
5	EBF1	chr7:102795725-102796440	GM12878	blood:	n/a	chr7:102795999-102796010
6	EBF1	chr7:102795806-102796232	GM12878	blood:	n/a	chr7:102795999-102796010

Variant related genes	Relation type
ENSG00000236848	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10266523	0.82[JPT][hapmap]
rs10486853	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11760826	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs11978339	0.82[JPT][hapmap]
rs12154780	0.85[AFR][1000 genomes]
rs13224269	0.94[ASN][1000 genomes]
rs13229230	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13229368	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13237057	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1404213	0.80[ASW][hapmap]
rs1477160	0.81[ASW][hapmap]
rs17136078	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17136079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17136083	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17136728	0.82[JPT][hapmap]
rs17606134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17680523	0.92[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs17837510	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1861725	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs1861731	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1861732	0.91[AFR][1000 genomes]
rs1968200	0.94[ASN][1000 genomes]
rs1968201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1968203	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1968204	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2193420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2878	0.82[JPT][hapmap]
rs3087615	0.92[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs3987913	0.92[ASN][1000 genomes]
rs3987937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4266582	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4336542	0.92[ASN][1000 genomes]
rs4360229	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428604	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4480047	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4523183	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4593456	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4727563	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4727566	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4727568	0.86[CHB][hapmap]
rs4729872	0.87[ASW][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.83[YRI][hapmap]
rs4729875	0.82[YRI][hapmap]
rs4729885	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729886	0.94[ASN][1000 genomes]
rs4729887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4729889	0.92[ASN][1000 genomes]
rs4729890	0.92[ASN][1000 genomes]
rs4729891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4729896	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4729899	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4729911	0.92[CEU][hapmap]
rs5025411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56711496	0.94[ASN][1000 genomes]
rs57125388	0.94[ASN][1000 genomes]
rs58962103	0.94[ASN][1000 genomes]
rs61581136	0.94[ASN][1000 genomes]
rs61591042	0.94[ASN][1000 genomes]
rs62480085	0.92[ASN][1000 genomes]
rs62480090	0.94[ASN][1000 genomes]
rs62480132	0.92[ASN][1000 genomes]
rs62480133	0.92[ASN][1000 genomes]
rs62480134	0.92[ASN][1000 genomes]
rs62481562	0.81[ASN][1000 genomes]
rs62481564	0.94[ASN][1000 genomes]
rs62481612	0.94[ASN][1000 genomes]
rs62481613	0.94[ASN][1000 genomes]
rs62481614	0.89[ASN][1000 genomes]
rs62481615	0.81[ASN][1000 genomes]
rs62481648	0.94[ASN][1000 genomes]
rs62481654	0.81[ASN][1000 genomes]
rs62481655	0.89[ASN][1000 genomes]
rs62484774	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62484781	0.94[ASN][1000 genomes]
rs62484782	0.94[ASN][1000 genomes]
rs62484783	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62484784	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6465905	0.84[LWK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs6950177	0.80[ASW][hapmap]
rs6971734	0.82[JPT][hapmap]
rs6973702	0.81[ASW][hapmap]
rs7455141	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7777392	0.82[CHB][hapmap]
rs7782147	0.83[AFR][1000 genomes]
rs7783856	0.80[ASW][hapmap]
rs7784337	0.80[ASW][hapmap]
rs9640672	0.84[AFR][1000 genomes]
rs9641308	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv831084	chr7:102778908-102964970	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv966872	chr7:102791751-102798505	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3372063	chr7:102793600-102796412	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7804020	RP11-401L13.5	cis	Thyroid	GTEx
rs7804020	DPY19L2P2	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102790200-102803200	Weak transcription	Gastric	stomach
2	chr7:102790400-102796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:102790800-102796200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:102791000-102796200	Weak transcription	Spleen	Spleen
5	chr7:102792200-102796000	Weak transcription	Small Intestine	intestine
6	chr7:102793400-102796000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:102794200-102796000	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:102794600-102796000	Weak transcription	Brain Anterior Caudate	brain
9	chr7:102794600-102796000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:102794800-102798600	Weak transcription	K562	blood
11	chr7:102794800-102803200	Weak transcription	Fetal Intestine Large	intestine
12	chr7:102795400-102796400	Active TSS	GM12878-XiMat	blood
13	chr7:102795600-102796000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:102795800-102796000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:102795800-102796000	Enhancers	Primary B cells from peripheral blood	blood
16	chr7:102795800-102796000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr7:102795800-102796000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr7:102795800-102796000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr7:102795800-102796000	Flanking Active TSS	Liver	Liver
20	chr7:102795800-102796400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:102795800-102796800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links