Variant report

Variant	rs2158877
Chromosome Location	chr7:22305444-22305445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:22292377..22294124-chr7:22302875..22305732,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10227259	0.85[JPT][hapmap]
rs10242605	0.88[JPT][hapmap]
rs10242851	0.85[JPT][hapmap]
rs10268485	0.88[JPT][hapmap]
rs10276593	0.80[JPT][hapmap]
rs10499545	0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs10499555	0.81[AMR][1000 genomes]
rs11975330	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11980801	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs12333620	0.81[JPT][hapmap]
rs12534599	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs13239365	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs1345252	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs1543886	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs1568571	0.80[JPT][hapmap]
rs1568572	0.80[JPT][hapmap]
rs1636895	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17146447	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs17146449	0.81[AMR][1000 genomes]
rs17146497	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1798803	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2256891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2528644	0.84[ASN][1000 genomes]
rs2528913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2528914	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2528916	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2528917	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2528918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686469	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2686499	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686528	0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs34078437	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62447068	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779510	0.86[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs7796489	0.88[JPT][hapmap]
rs7798671	0.88[JPT][hapmap]
rs7799625	0.80[JPT][hapmap]
rs7805084	0.81[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1815409	chr7:22296017-22315855	Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2158877	DNAH11	cis	cerebellum	SCAN
rs2158877	HNRNPA2B1	cis	parietal	SCAN
rs2158877	IFITM3	trans	lymphoblastoid	seeQTL
rs2158877	CCDC126	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:22243400-22307200	Weak transcription	Thymus	Thymus
2	chr7:22262200-22329000	Weak transcription	Primary B cells from cord blood	blood
3	chr7:22278600-22325800	Weak transcription	Liver	Liver
4	chr7:22278800-22310800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:22282200-22309000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:22282200-22364400	Weak transcription	Esophagus	oesophagus
7	chr7:22291800-22308200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:22296000-22307200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:22296000-22309000	Weak transcription	Fetal Intestine Large	intestine
10	chr7:22296000-22309400	Weak transcription	Pancreas	Pancrea
11	chr7:22296400-22308800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr7:22296600-22307800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:22296800-22307400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:22297200-22307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:22297200-22309000	Weak transcription	Fetal Intestine Small	intestine
16	chr7:22297400-22309800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:22297400-22309800	Weak transcription	NHEK	skin
18	chr7:22300000-22307400	Weak transcription	Fetal Thymus	thymus
19	chr7:22302200-22306000	Strong transcription	Dnd41	blood
20	chr7:22304000-22306200	Strong transcription	HepG2	liver
21	chr7:22304200-22308600	Weak transcription	Rectal Mucosa Donor 31	rectum

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