Variant report

Variant	rs3758078
Chromosome Location	chr8:86374664-86374665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:86363678..86364494-chr8:86374198..86374980,2	MCF-7	breast:
2	chr8:86373793..86376899-chr8:86998896..87001584,3	MCF-7	breast:
3	chr22:36782277..36784307-chr8:86374266..86376495,2	MCF-7	breast:
4	chr8:86372229..86378702-chr8:86846475..86858080,32	MCF-7	breast:
5	chr8:86372586..86374669-chr8:86379787..86381546,2	MCF-7	breast:
6	chr8:86373353..86377706-chr8:86848632..86856784,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253154	Chromatin interaction
ENSG00000147614	Chromatin interaction
ENSG00000100345	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10088136	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10095352	0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10111039	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10504812	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs10504813	0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10907474	0.87[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11261474	0.84[JPT][hapmap]
rs11780285	0.97[ASN][1000 genomes]
rs11985733	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs13252971	0.84[JPT][hapmap]
rs13255540	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13273654	0.80[EUR][1000 genomes]
rs1389245	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1389247	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1472360	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1493302	0.84[JPT][hapmap]
rs1496529	0.84[JPT][hapmap]
rs1496530	0.84[JPT][hapmap]
rs1532423	0.80[CEU][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs1532424	0.84[JPT][hapmap]
rs17042	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1845253	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1995056	0.89[JPT][hapmap]
rs2055077	0.86[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs20571	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs2072696	0.81[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2307075	0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2403105	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453868	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2548281	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2645049	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs2645053	0.81[ASN][1000 genomes]
rs3087782	0.90[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs359535	0.91[CHD][hapmap]
rs3758076	0.80[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3758077	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4566	0.80[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4740053	0.91[CHD][hapmap]
rs55641432	0.98[ASN][1000 genomes]
rs55929157	0.98[ASN][1000 genomes]
rs58958691	0.97[ASN][1000 genomes]
rs66498753	0.81[ASN][1000 genomes]
rs67824746	0.98[ASN][1000 genomes]
rs6988475	0.80[CEU][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6997458	0.80[CEU][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs7000950	0.81[EUR][1000 genomes]
rs7016369	0.87[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs703	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs713488	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs713489	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7386162	0.97[ASN][1000 genomes]
rs9286249	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs931505	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9329911	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs955007	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9969643	0.80[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9987281	0.84[JPT][hapmap]
rs999466	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv3361413	chr8:86374200-86377398	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3758078	CA2	cis	multi-tissue	Pritchard
rs3758078	CA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86354400-86375400	Weak transcription	Psoas Muscle	Psoas
2	chr8:86358400-86375600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:86366600-86375000	Weak transcription	HMEC	breast
4	chr8:86366600-86375200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:86366800-86375200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr8:86366800-86375200	Weak transcription	NHEK	skin
7	chr8:86367600-86375600	Weak transcription	Gastric	stomach
8	chr8:86368400-86375400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr8:86368600-86375600	Weak transcription	Esophagus	oesophagus
10	chr8:86369200-86375400	Enhancers	Primary B cells from cord blood	blood
11	chr8:86370400-86375400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr8:86371800-86375200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr8:86371800-86375200	Weak transcription	Colon Smooth Muscle	Colon
14	chr8:86372000-86375400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr8:86372200-86375200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr8:86372200-86375200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr8:86372200-86375400	Weak transcription	Primary T cells from cord blood	blood
18	chr8:86372200-86375400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr8:86372400-86374800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr8:86372400-86375200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr8:86373400-86374800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr8:86373600-86374800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr8:86373800-86375200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr8:86373800-86375200	Enhancers	Brain Angular Gyrus	brain
25	chr8:86373800-86375200	Enhancers	Brain Anterior Caudate	brain
26	chr8:86373800-86375200	Enhancers	Brain Hippocampus Middle	brain
27	chr8:86373800-86375400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr8:86373800-86375400	Enhancers	Fetal Lung	lung
29	chr8:86374000-86375000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr8:86374000-86375000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr8:86374000-86375200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr8:86374000-86375200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr8:86374000-86375200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr8:86374000-86375200	Enhancers	Brain Substantia Nigra	brain
35	chr8:86374000-86375200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr8:86374000-86375400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr8:86374000-86375400	Enhancers	Adipose Nuclei	Adipose
38	chr8:86374000-86375400	Enhancers	Brain Cingulate Gyrus	brain
39	chr8:86374000-86375600	Enhancers	Stomach Mucosa	stomach
40	chr8:86374200-86374800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr8:86374200-86375400	Weak transcription	Colonic Mucosa	Colon
42	chr8:86374400-86375200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
43	chr8:86374400-86375200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr8:86374400-86375200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr8:86374400-86375400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr8:86374400-86375600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr8:86374600-86374800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
48	chr8:86374600-86374800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr8:86374600-86375200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr8:86374600-86375400	Enhancers	Primary hematopoietic stem cells	blood

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