Variant report

Variant	rs29233
Chromosome Location	chr6:29611229-29611230
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29599418..29601085-chr6:29610262..29612133,2	K562	blood:
2	chr6:29610699..29612322-chr6:29612804..29615708,2	K562	blood:
3	chr6:29598626..29603210-chr6:29607516..29611410,5	K562	blood:
4	chr6:29609719..29612322-chr6:29612804..29614354,2	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs16895218	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17184661	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2057010	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs29219	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs29254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025628	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3025642	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3117313	0.92[ASN][1000 genomes]
rs3888722	1.00[AFR][1000 genomes]
rs3906306	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4085262	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4085264	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4143366	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55661776	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55672647	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55693745	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55792521	0.82[ASN][1000 genomes]
rs55884048	1.00[AFR][1000 genomes]
rs55933609	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56044823	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs56045105	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56101454	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56142919	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56155438	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56155978	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56172386	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56269224	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56287651	1.00[AFR][1000 genomes]
rs56290866	1.00[AFR][1000 genomes]
rs56392172	1.00[AFR][1000 genomes]
rs56393713	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62391766	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62391767	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62391768	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62391770	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62391785	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62391786	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62391801	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62391819	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62391822	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62391833	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62391835	1.00[AFR][1000 genomes]
rs62391842	1.00[AFR][1000 genomes]
rs62391843	1.00[AFR][1000 genomes]
rs62391844	1.00[AFR][1000 genomes]
rs62391850	1.00[AFR][1000 genomes]
rs62391851	1.00[AFR][1000 genomes]
rs62392946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392949	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392950	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62392951	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392953	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392954	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392955	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392956	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392957	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392958	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62394668	1.00[AFR][1000 genomes]
rs62394669	1.00[AFR][1000 genomes]
rs62394670	1.00[AFR][1000 genomes]
rs62406580	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62406583	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67382831	1.00[AFR][1000 genomes]
rs71550159	1.00[AFR][1000 genomes]
rs9461540	0.83[ASN][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv969292	chr6:29604881-29612154	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs29233	HLA-H	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29608400-29611600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr6:29608400-29616400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:29609600-29617200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:29609800-29615600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:29609800-29615600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:29610000-29611400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:29610000-29611600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:29610000-29615400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:29610000-29615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:29610000-29615400	Weak transcription	HMEC	breast
11	chr6:29610000-29615400	Weak transcription	NHEK	skin
12	chr6:29610000-29615600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:29610000-29617200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:29610600-29617200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:29610600-29617400	Weak transcription	K562	blood
16	chr6:29610800-29617200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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