Variant report

Variant	rs9461015
Chromosome Location	chr6:24449020-24449021
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24447065..24450391-chr6:24494132..24495678,3	K562	blood:
2	chr6:24431522..24434175-chr6:24447084..24450027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10946700	1.00[ASN][1000 genomes]
rs10946701	0.81[ASN][1000 genomes]
rs12194966	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12198188	1.00[ASN][1000 genomes]
rs12524609	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13191455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13192752	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13205577	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17247566	0.81[ASN][1000 genomes]
rs34089102	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35901848	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3846833	0.81[ASN][1000 genomes]
rs60830931	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62400468	0.81[ASN][1000 genomes]
rs6922313	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6922631	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71544274	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7762593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762901	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766620	0.81[ASN][1000 genomes]
rs9295624	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461010	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9461011	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461012	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461013	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467148	1.00[ASN][1000 genomes]
rs9467157	1.00[ASN][1000 genomes]
rs9467158	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467160	1.00[ASN][1000 genomes]
rs9467161	1.00[ASN][1000 genomes]
rs9467166	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467170	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467171	0.81[ASN][1000 genomes]
rs9467172	0.81[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	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9461015	HIST1H2AG	cis	cerebellum	SCAN
rs9461015	ALDH5A1	cis	cerebellum	SCAN
rs9461015	HIST1H2BM	cis	parietal	SCAN
rs9461015	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24417400-24451800	Strong transcription	Liver	Liver
2	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
3	chr6:24424000-24456600	Weak transcription	Ovary	ovary
4	chr6:24427600-24456800	Weak transcription	Lung	lung
5	chr6:24427800-24467000	Weak transcription	Brain Germinal Matrix	brain
6	chr6:24428200-24449400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
8	chr6:24429200-24455600	Weak transcription	Brain Angular Gyrus	brain
9	chr6:24429400-24483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:24429600-24455000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:24432600-24463800	Weak transcription	Fetal Intestine Small	intestine
12	chr6:24433600-24451600	Weak transcription	Adipose Nuclei	Adipose
13	chr6:24437600-24455400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:24437800-24450600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:24437800-24459600	Weak transcription	Left Ventricle	heart
16	chr6:24438000-24464000	Weak transcription	Pancreas	Pancrea
17	chr6:24438200-24455600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:24438400-24483200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:24438600-24459800	Weak transcription	Fetal Stomach	stomach
20	chr6:24438800-24469200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:24440400-24452000	Weak transcription	Primary T cells from cord blood	blood
22	chr6:24441400-24452000	Weak transcription	Thymus	Thymus
23	chr6:24442000-24452000	Weak transcription	Fetal Thymus	thymus
24	chr6:24444000-24449200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:24444000-24458200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:24446000-24449200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:24446400-24449400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:24446400-24451600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:24446400-24451800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:24447200-24470200	Weak transcription	Aorta	Aorta
31	chr6:24447400-24490400	Weak transcription	Brain Anterior Caudate	brain
32	chr6:24448200-24466200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:24448400-24452000	Weak transcription	K562	blood
34	chr6:24448400-24458000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:24448800-24449400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:24448800-24450000	Active TSS	Gastric	stomach
37	chr6:24448800-24450200	Enhancers	Esophagus	oesophagus
38	chr6:24448800-24488000	Weak transcription	Fetal Muscle Leg	muscle

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