Variant report

Variant	rs29254
Chromosome Location	chr6:29623594-29623595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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]
rs29233	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	nsv527037	chr6:29615822-29624112	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs29254	HLA-H	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29618000-29624000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29618400-29624000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:29618400-29624000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:29618400-29624600	Weak transcription	Right Atrium	heart
5	chr6:29618400-29629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:29618400-29629600	Weak transcription	Right Ventricle	heart
7	chr6:29618600-29624600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:29620000-29628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:29620000-29631200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:29620200-29624200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:29620600-29626600	Enhancers	Fetal Heart	heart
12	chr6:29620800-29624000	Enhancers	Brain Angular Gyrus	brain
13	chr6:29621000-29624000	Enhancers	Brain Substantia Nigra	brain
14	chr6:29621000-29625000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:29621600-29624000	Enhancers	Brain Cingulate Gyrus	brain
16	chr6:29621800-29625000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr6:29622000-29624200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:29622800-29624600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:29622800-29624800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr6:29622800-29625000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:29623000-29624000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:29623200-29623600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:29623200-29623600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr6:29623200-29623600	Enhancers	Left Ventricle	heart
25	chr6:29623200-29623600	Enhancers	GM12878-XiMat	blood
26	chr6:29623200-29624600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr6:29623200-29625200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:29623400-29624000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:29623400-29624400	Enhancers	Stomach Smooth Muscle	stomach
30	chr6:29623400-29624800	Enhancers	Aorta	Aorta
31	chr6:29623400-29625000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:29623400-29630600	Active TSS	Brain Anterior Caudate	brain

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