Variant report

Variant	rs9969643
Chromosome Location	chr8:86365987-86365988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:86365526..86368719-chr8:87353659..87355514,3	MCF-7	breast:
2	chr8:86364193..86367420-chr8:86983302..86985481,3	MCF-7	breast:
3	chr8:86364996..86367147-chr8:86853567..86855147,2	MCF-7	breast:
4	chr8:86362726..86365485-chr8:86365567..86367420,2	K562	blood:
5	chr8:86365982..86366575-chr8:86985503..86986224,2	MCF-7	breast:
6	chr8:86364243..86366553-chr8:86374714..86377959,3	MCF-7	breast:
7	chr8:86364795..86367348-chr8:86976708..86978928,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253549	Chromatin interaction
ENSG00000123124	Chromatin interaction
ENSG00000104267	Chromatin interaction
ENSG00000254231	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10087278	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10088136	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10091566	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10095352	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10111039	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10504812	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10504813	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10907474	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11261471	0.86[JPT][hapmap]
rs11261474	0.84[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11780285	0.80[ASN][1000 genomes]
rs11985029	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11985733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12541445	0.86[JPT][hapmap]
rs12543256	0.82[JPT][hapmap]
rs12544332	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12550814	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1303806	0.95[JPT][hapmap]
rs13252971	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1390711	0.95[JPT][hapmap]
rs1390712	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1493302	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1496529	1.00[JPT][hapmap]
rs1496530	1.00[JPT][hapmap]
rs1496531	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1496532	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1532423	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs1532424	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1543852	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1553015	0.95[JPT][hapmap]
rs16913721	0.91[JPT][hapmap]
rs17042	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs1845253	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1908075	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1995056	0.90[JPT][hapmap]
rs1995057	0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1995058	0.95[JPT][hapmap]
rs2006767	0.91[JPT][hapmap]
rs2055077	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs20571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2072696	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2173044	0.80[EUR][1000 genomes]
rs2279701	0.86[JPT][hapmap]
rs2291787	0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2307075	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2403104	0.95[JPT][hapmap]
rs2548281	0.88[CEU][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2645049	0.95[JPT][hapmap]
rs3087782	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3758076	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758077	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758078	0.80[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808539	0.95[JPT][hapmap]
rs4566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4609189	0.82[JPT][hapmap]
rs4739700	0.91[JPT][hapmap]
rs4740049	0.95[JPT][hapmap]
rs55641432	0.84[ASN][1000 genomes]
rs55929157	0.84[ASN][1000 genomes]
rs58958691	0.80[ASN][1000 genomes]
rs67824746	0.84[ASN][1000 genomes]
rs6988475	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6993387	0.91[JPT][hapmap]
rs6994113	0.82[JPT][hapmap]
rs6997458	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs7001359	0.86[JPT][hapmap]
rs7008772	0.91[JPT][hapmap]
rs7011926	0.95[JPT][hapmap]
rs7016369	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs703	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs725605	0.83[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7386162	0.80[ASN][1000 genomes]
rs7818163	0.91[JPT][hapmap]
rs7824715	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs903895	0.95[JPT][hapmap]
rs903896	0.95[JPT][hapmap]
rs903897	0.95[JPT][hapmap]
rs9286249	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs931505	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs955007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9987281	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs999466	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022463	chr8:86257031-86547831	Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1804888	chr8:86263098-86986703	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv831377	chr8:86263107-86444141	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1028148	chr8:86310570-86553130	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv2761206	chr8:86310582-86468868	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9969643	RALYL	cis	parietal	SCAN
rs9969643	CA2	cis	multi-tissue	Pritchard
rs9969643	C8orf59	cis	cerebellum	SCAN
rs9969643	CA2	Cis_1M	lymphoblastoid	RTeQTL
rs9969643	CA2	cis	lymphoblastoid	seeQTL
rs9969643	CA13	cis	Lymphoblastoid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86351200-86367200	Weak transcription	Left Ventricle	heart
2	chr8:86351200-86374000	Weak transcription	Fetal Intestine Small	intestine
3	chr8:86351600-86368200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr8:86354400-86375400	Weak transcription	Psoas Muscle	Psoas
5	chr8:86358400-86375600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:86360400-86366000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:86364200-86366800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:86365200-86366800	Enhancers	Brain Anterior Caudate	brain
9	chr8:86365200-86373200	Weak transcription	Liver	Liver
10	chr8:86365400-86366600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:86365400-86366800	Enhancers	Brain Substantia Nigra	brain
12	chr8:86365400-86368400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr8:86365800-86366600	Enhancers	Brain Hippocampus Middle	brain
14	chr8:86365800-86366600	Enhancers	HMEC	breast
15	chr8:86365800-86366800	Enhancers	NHEK	skin

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