Variant report

Variant	rs6682659
Chromosome Location	chr1:226214882-226214883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226208374..226211010-chr1:226213387..226217163,4	K562	blood:
2	chr1:226205369..226210756-chr1:226213268..226218237,7	K562	blood:
3	chr1:226213056..226215448-chr1:226250326..226252593,2	K562	blood:
4	chr1:226187874..226190820-chr1:226213394..226216312,2	K562	blood:
5	chr1:226192599..226195198-chr1:226214634..226216846,2	K562	blood:
6	chr1:226213068..226214895-chr1:226247410..226249127,2	K562	blood:

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10157179	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10753411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799333	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10799334	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10915918	0.80[ASN][1000 genomes]
rs10915920	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915921	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10915923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915927	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12128917	0.87[EUR][1000 genomes]
rs12728713	0.82[GIH][hapmap]
rs12743653	0.82[GIH][hapmap]
rs1877158	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001307	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4477241	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4604663	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653438	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[EUR][1000 genomes]
rs4653439	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653703	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653704	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653705	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653706	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426096	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6426098	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6426099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6675606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6693325	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6701318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73100558	0.93[EUR][1000 genomes]
rs7549940	0.88[AFR][1000 genomes]
rs7550220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7553984	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9701639	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6682659	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs6682659	FBXO28	cis	cerebellum	SCAN
rs6682659	H3F3A	cis	Esophagus Mucosa	GTEx
rs6682659	H3F3A	cis	Nerve Tibial	GTEx
rs6682659	H3F3A	cis	Artery Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226205600-226215000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:226207800-226215400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:226210200-226215000	Weak transcription	Stomach Mucosa	stomach
4	chr1:226210200-226215200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:226210200-226215600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:226210400-226215000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:226213000-226215000	Weak transcription	Colonic Mucosa	Colon
8	chr1:226214400-226217600	Enhancers	K562	blood
9	chr1:226214800-226216400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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