Variant report

Variant	rs6578611
Chromosome Location	chr11:5369776-5369777
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	TCF7L2	chr11:5369768-5370092	Hela-S3	cervix:	n/a	n/a
2	GATA1	chr11:5369533-5370252	PBDE	blood:	n/a	chr11:5369630-5369642

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5337010..5339667-chr11:5367362..5370323,2	K562	blood:
2	chr11:5369590..5371367-chr11:5374637..5376973,2	K562	blood:

Variant related genes	Relation type
OR51B6	TF binding region
OR51B5	TF binding region
ENSG00000230087	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10768807	0.86[GIH][hapmap]
rs10768828	0.84[JPT][hapmap]
rs10768830	0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs10837853	0.84[CHD][hapmap];0.91[GIH][hapmap]
rs10837867	0.84[JPT][hapmap]
rs10837868	0.84[JPT][hapmap]
rs10837870	0.84[JPT][hapmap]
rs10837871	0.84[JPT][hapmap]
rs10837872	0.81[JPT][hapmap]
rs10837873	0.82[JPT][hapmap]
rs10837874	0.84[JPT][hapmap]
rs11036912	0.88[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11036923	0.82[JPT][hapmap]
rs11036924	0.84[JPT][hapmap]
rs11036925	0.84[JPT][hapmap]
rs11036927	0.84[JPT][hapmap]
rs11036930	0.84[JPT][hapmap]
rs11036936	0.84[JPT][hapmap]
rs11603059	0.82[JPT][hapmap]
rs11604883	0.82[JPT][hapmap]
rs12275713	0.84[JPT][hapmap]
rs12796030	0.84[JPT][hapmap]
rs12801179	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs17270517	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs17270776	0.84[JPT][hapmap]
rs17270818	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs17270832	0.83[JPT][hapmap]
rs17270894	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs17356445	0.83[JPT][hapmap]
rs2467232	0.84[JPT][hapmap]
rs2647598	0.84[JPT][hapmap]
rs2647599	0.84[JPT][hapmap]
rs2647600	0.84[JPT][hapmap]
rs2647601	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs2647606	0.82[JPT][hapmap]
rs2723380	0.84[JPT][hapmap]
rs2723387	0.84[JPT][hapmap]
rs2736553	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs2736555	0.84[JPT][hapmap]
rs2736557	0.84[JPT][hapmap]
rs2736560	0.84[JPT][hapmap]
rs2736561	0.84[JPT][hapmap]
rs2736565	0.84[JPT][hapmap]
rs4255565	0.82[JPT][hapmap]
rs4304811	0.84[JPT][hapmap]
rs4312094	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4326830	0.84[JPT][hapmap]
rs4495917	0.84[JPT][hapmap]
rs4910551	0.87[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4910552	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4910757	0.84[JPT][hapmap]
rs4910760	0.84[JPT][hapmap]
rs4910762	0.84[JPT][hapmap]
rs4910765	0.82[JPT][hapmap]
rs4910770	0.84[JPT][hapmap]
rs4910771	0.82[JPT][hapmap]
rs5024037	0.84[JPT][hapmap]
rs6578610	0.83[CHB][hapmap]
rs7109909	1.00[JPT][hapmap]
rs7114155	0.80[ASN][1000 genomes]
rs7929631	0.84[JPT][hapmap]
rs884222	0.84[JPT][hapmap]

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	nsv524400	chr11:5328361-5416622	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv896931	chr11:5357881-5505149	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6578611	TRIM22	cis	parietal	SCAN
rs6578611	SLC22A18AS	cis	cerebellum	SCAN
rs6578611	ZNF562	trans	parietal	SCAN
rs6578611	KRTAP5-2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5365600-5382600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:5367600-5371000	Weak transcription	Osteobl	bone
3	chr11:5368200-5369800	Weak transcription	K562	blood
4	chr11:5369600-5370000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr11:5369600-5370000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr11:5369600-5370200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr11:5369600-5370200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:5369600-5371000	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links