Variant report

Variant	rs2297980
Chromosome Location	chr6:54173413-54173414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10085239	0.86[GIH][hapmap]
rs10948810	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150873	1.00[JPT][hapmap]
rs12191165	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193042	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198031	0.85[CEU][hapmap]
rs12198070	0.85[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs12199953	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201064	1.00[ASN][1000 genomes]
rs12201103	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208501	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs12212836	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1298143	0.84[CEU][hapmap]
rs1340660	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417390	1.00[JPT][hapmap]
rs16885122	0.85[CEU][hapmap]
rs16885246	1.00[JPT][hapmap]
rs16885273	1.00[ASW][hapmap]
rs17681477	0.84[CEU][hapmap]
rs1934790	0.85[CEU][hapmap]
rs2754813	1.00[JPT][hapmap]
rs2792644	1.00[JPT][hapmap]
rs6937514	0.84[CEU][hapmap]
rs73442548	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741347	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs843827	1.00[JPT][hapmap]
rs9296744	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs9349700	0.82[CEU][hapmap]
rs9357793	0.85[CEU][hapmap]
rs9357795	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs9367556	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs9370276	0.84[CEU][hapmap]
rs9370290	0.85[YRI][hapmap]
rs9382311	0.84[CEU][hapmap]
rs9395920	0.83[CEU][hapmap]
rs9885789	0.85[CEU][hapmap];0.84[TSI][hapmap]

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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2297980	TINAG	cis	parietal	SCAN
rs2297980	IL17A	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54168800-54176400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:54171800-54173800	Enhancers	HepG2	liver
3	chr6:54171800-54176600	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:54172200-54176200	Active TSS	Fetal Kidney	kidney
5	chr6:54172400-54176600	Active TSS	Duodenum Mucosa	Duodenum
6	chr6:54172600-54175200	Active TSS	Rectal Smooth Muscle	rectum
7	chr6:54172600-54176200	Active TSS	Colonic Mucosa	Colon
8	chr6:54172800-54173600	Enhancers	A549	lung
9	chr6:54172800-54176600	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr6:54173000-54178000	Active TSS	Fetal Intestine Large	intestine
11	chr6:54173000-54178200	Active TSS	Fetal Intestine Small	intestine
12	chr6:54173200-54174200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr6:54173400-54173800	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links