Variant report

Variant	rs2071653
Chromosome Location	chr6:29635928-29635929
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	chr6:29634001..29636635-chr6:29639490..29642126,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1611371	0.80[ASN][1000 genomes]
rs1611380	0.80[ASN][1000 genomes]
rs2071652	0.83[ASN][1000 genomes]
rs3095285	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095291	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3095292	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3116798	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3117290	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129029	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129043	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129190	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3131854	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905408	0.83[ASN][1000 genomes]
rs9257940	0.83[ASN][1000 genomes]
rs9257953	0.83[ASN][1000 genomes]
rs9257986	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2071653	HLA-F	cis	lymphoblastoid	seeQTL
rs2071653	HLA-F	cis	multi-tissue	Pritchard
rs2071653	FKSG83	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29630800-29643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:29631400-29640200	Weak transcription	NHEK	skin
4	chr6:29632000-29636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:29632000-29638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:29633400-29636000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:29633400-29636400	Enhancers	Fetal Heart	heart
8	chr6:29633600-29636600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:29633800-29636600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr6:29634000-29636200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:29634400-29636200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:29634600-29636400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:29634600-29641000	Weak transcription	Brain Anterior Caudate	brain
14	chr6:29634600-29642000	Weak transcription	Brain Angular Gyrus	brain
15	chr6:29634800-29636200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:29635000-29636000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:29635000-29636400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:29635200-29636600	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr6:29635400-29636200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:29635600-29636200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:29635600-29636600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:29635600-29636600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr6:29635600-29639600	Strong transcription	Brain Substantia Nigra	brain
24	chr6:29635800-29636000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:29635800-29636400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:29635800-29636600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:29635800-29636600	Strong transcription	Brain Hippocampus Middle	brain

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