Variant report

Variant	rs7176652
Chromosome Location	chr15:93494978-93494979
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	chr15:93445552..93447939-chr15:93494281..93496806,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264173	Chromatin interaction
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10520716	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs10520718	0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1074512	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11074120	0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857466	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11857669	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12437674	0.92[CHB][hapmap]
rs12443243	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs12591124	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12592920	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12594474	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12914956	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1318689	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1320819	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs1406714	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs17610487	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1881834	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1881835	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes]
rs2304655	0.86[JPT][hapmap]
rs2388055	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34448107	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36032658	0.82[EUR][1000 genomes]
rs3736619	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3784785	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3826035	0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs3826036	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs4327000	0.93[CHB][hapmap]
rs4778052	0.83[CHB][hapmap]
rs62023146	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6497010	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6497011	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6497013	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7164668	0.86[CHB][hapmap]
rs7167194	0.84[CHB][hapmap]
rs7173103	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs7174043	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7179863	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8024528	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs8026679	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8026695	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs8035739	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs8042395	0.93[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042632	0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs920389	0.84[CHB][hapmap]
rs9302362	0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs961233	0.86[JPT][hapmap]

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	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7176652	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93474800-93501800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:93477200-93501200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:93478600-93503200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:93486000-93495000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:93487600-93500000	Strong transcription	Brain Angular Gyrus	brain
6	chr15:93491600-93498400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:93493000-93500400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:93493000-93508600	Strong transcription	Hela-S3	cervix
9	chr15:93493200-93495800	Weak transcription	Pancreas	Pancrea
10	chr15:93493200-93499800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:93493200-93503800	Strong transcription	Brain Substantia Nigra	brain
12	chr15:93493200-93504400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:93493200-93504800	Strong transcription	Fetal Kidney	kidney
14	chr15:93493200-93508200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:93493200-93512200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:93493200-93533000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:93493200-93536000	Strong transcription	HSMM	muscle
18	chr15:93493200-93571000	Strong transcription	Dnd41	blood
19	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr15:93493400-93495800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:93493400-93495800	Weak transcription	Right Ventricle	heart
22	chr15:93493400-93495800	Weak transcription	Stomach Mucosa	stomach
23	chr15:93493400-93495800	Weak transcription	Spleen	Spleen
24	chr15:93493400-93496000	Weak transcription	Psoas Muscle	Psoas
25	chr15:93493400-93497200	Strong transcription	Brain Germinal Matrix	brain
26	chr15:93493400-93498200	Strong transcription	Fetal Stomach	stomach
27	chr15:93493400-93500400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr15:93493400-93500400	Strong transcription	NHDF-Ad	bronchial
29	chr15:93493400-93500600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
30	chr15:93493400-93500600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:93493400-93500600	Strong transcription	NH-A	brain
32	chr15:93493400-93501400	Strong transcription	HSMMtube	muscle
33	chr15:93493400-93501600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:93493400-93501600	Strong transcription	Brain Hippocampus Middle	brain
35	chr15:93493400-93501800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:93493400-93503000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:93493400-93504800	Strong transcription	Brain Anterior Caudate	brain
38	chr15:93493400-93505000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr15:93493400-93505800	Strong transcription	Fetal Lung	lung
40	chr15:93493400-93508200	Strong transcription	Primary B cells from cord blood	blood
41	chr15:93493400-93508400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:93493400-93511800	Strong transcription	Adipose Nuclei	Adipose
43	chr15:93493400-93511800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr15:93493400-93568600	Strong transcription	Liver	Liver
46	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
47	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr15:93493600-93501000	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr15:93493600-93504800	Strong transcription	H1 Cell Line	embryonic stem cell

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