Variant report

Variant	rs6988475
Chromosome Location	chr8:86383268-86383269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86375875..86379086-chr8:86380688..86384617,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104267	Chromatin interaction
ENSG00000253549	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10087278	0.91[EUR][1000 genomes]
rs10088136	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10091566	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10095352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10111039	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10504812	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10504813	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10907474	0.88[CEU][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11261471	0.86[JPT][hapmap]
rs11261474	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs11780285	0.84[ASN][1000 genomes]
rs11985029	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11985733	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12541445	0.86[JPT][hapmap]
rs12543256	0.82[JPT][hapmap]
rs12544332	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12550814	0.82[EUR][1000 genomes]
rs1303806	0.95[JPT][hapmap]
rs13252971	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1390711	0.95[JPT][hapmap]
rs1390712	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1493302	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1496529	1.00[JPT][hapmap]
rs1496530	1.00[JPT][hapmap]
rs1496531	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1496532	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1532423	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs1532424	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs1543852	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1553015	0.95[JPT][hapmap]
rs17042	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs1845253	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1908075	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1908762	0.82[JPT][hapmap]
rs1995056	0.95[JPT][hapmap]
rs1995057	0.86[JPT][hapmap]
rs1995058	0.95[JPT][hapmap]
rs2055077	0.95[JPT][hapmap]
rs20571	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2072696	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2279701	0.86[JPT][hapmap]
rs2291787	0.86[JPT][hapmap]
rs2307075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403104	0.95[JPT][hapmap]
rs2548281	0.88[CEU][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs2645049	0.95[JPT][hapmap]
rs3087782	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3758076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3758077	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3758078	0.80[CEU][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3808539	0.95[JPT][hapmap]
rs4566	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4609189	0.82[JPT][hapmap]
rs4739700	0.90[JPT][hapmap]
rs4740049	0.95[JPT][hapmap]
rs55641432	0.80[ASN][1000 genomes]
rs55929157	0.80[ASN][1000 genomes]
rs58958691	0.84[ASN][1000 genomes]
rs67824746	0.80[ASN][1000 genomes]
rs6997458	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs7001359	0.86[JPT][hapmap]
rs7011926	0.95[JPT][hapmap]
rs7016369	0.88[CEU][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs703	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs725605	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs7386162	0.84[ASN][1000 genomes]
rs7824715	0.80[EUR][1000 genomes]
rs903895	0.95[JPT][hapmap]
rs903896	0.95[JPT][hapmap]
rs903897	0.95[JPT][hapmap]
rs9286249	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931505	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs955007	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9969643	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]
rs9987281	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs999466	0.84[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
rs6988475	CA2	cis	lymphoblastoid	seeQTL
rs6988475	CA2	cis	multi-tissue	Pritchard
rs6988475	C8orf59	cis	cerebellum	SCAN
rs6988475	CA13	cis	Lymphoblastoid	GTEx
rs6988475	RALYL	cis	parietal	SCAN
rs6988475	CA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86377000-86394600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr8:86377600-86390800	Weak transcription	Right Ventricle	heart
3	chr8:86377600-86392600	Weak transcription	Psoas Muscle	Psoas
4	chr8:86377600-86395600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr8:86377600-86399000	Weak transcription	Fetal Heart	heart
6	chr8:86377800-86388200	Weak transcription	Adipose Nuclei	Adipose
7	chr8:86377800-86388400	Weak transcription	Lung	lung
8	chr8:86377800-86390200	Weak transcription	HMEC	breast
9	chr8:86378000-86384200	Weak transcription	Fetal Intestine Large	intestine
10	chr8:86378000-86385600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr8:86378000-86386600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr8:86378000-86388400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr8:86378000-86392800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr8:86378000-86392800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:86378000-86403000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr8:86378200-86387600	Weak transcription	NHEK	skin
17	chr8:86378200-86388400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr8:86378200-86389400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:86378200-86390600	Weak transcription	Brain Germinal Matrix	brain
20	chr8:86378600-86387000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr8:86379000-86393000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr8:86379600-86387600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr8:86380400-86394800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr8:86380600-86384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:86380600-86385400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr8:86380600-86386600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr8:86380600-86388600	Weak transcription	Fetal Stomach	stomach
28	chr8:86380600-86389400	Weak transcription	Colonic Mucosa	Colon
29	chr8:86380800-86385000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr8:86380800-86385600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr8:86381000-86383800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:86381000-86385600	Weak transcription	Right Atrium	heart
33	chr8:86381000-86386400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr8:86381000-86387000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr8:86381000-86387000	Weak transcription	Left Ventricle	heart
36	chr8:86381000-86388000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr8:86381000-86389200	Weak transcription	Gastric	stomach
38	chr8:86381000-86389200	Weak transcription	Pancreas	Pancrea
39	chr8:86381600-86384200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr8:86381800-86383600	Active TSS	Brain Angular Gyrus	brain
41	chr8:86382200-86384200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr8:86382400-86383800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr8:86382400-86385600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr8:86382400-86386000	Enhancers	Liver	Liver
45	chr8:86382400-86386200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr8:86382400-86386200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr8:86382400-86386800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr8:86382600-86383400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr8:86382600-86383400	Weak transcription	Brain Hippocampus Middle	brain
50	chr8:86382600-86383400	Weak transcription	Brain Substantia Nigra	brain

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