Variant report

Variant	rs3817597
Chromosome Location	chr15:93498105-93498106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93487564..93489597-chr15:93495946..93498208,2	MCF-7	breast:
2	chr15:93491122..93495072-chr15:93496449..93499929,5	K562	blood:
3	chr15:93449371..93451319-chr15:93496331..93498149,2	K562	blood:

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10520716	0.81[JPT][hapmap]
rs10520717	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs10520719	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11074126	0.82[AMR][1000 genomes]
rs11630052	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11630582	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11631553	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11632302	0.86[EUR][1000 genomes]
rs11632522	0.84[AMR][1000 genomes]
rs11634204	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11634207	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11634566	0.81[JPT][hapmap]
rs11637047	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11637185	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11857145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438635	0.81[JPT][hapmap]
rs12443243	0.81[JPT][hapmap]
rs12592920	0.82[JPT][hapmap]
rs12594991	0.90[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs12901950	0.82[CEU][hapmap];0.93[MEX][hapmap]
rs12904680	0.82[CEU][hapmap]
rs12906132	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12907579	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12915072	0.82[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs12916015	0.86[CEU][hapmap];0.93[MEX][hapmap]
rs1318689	0.81[JPT][hapmap]
rs1320819	0.81[JPT][hapmap]
rs1406714	0.81[JPT][hapmap]
rs1534779	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17525800	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2033844	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2119010	0.93[MEX][hapmap]
rs2272457	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2272459	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28668136	0.85[AMR][1000 genomes]
rs34026217	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35477598	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35596808	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs36048863	0.84[AMR][1000 genomes]
rs3784786	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3826035	0.87[JPT][hapmap]
rs4778062	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4778065	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56358327	0.85[AMR][1000 genomes]
rs7173103	0.81[JPT][hapmap]
rs8026695	0.81[JPT][hapmap]
rs8035739	0.81[JPT][hapmap]
rs961233	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3817597	ZNF710	cis	parietal	SCAN
rs3817597	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr15:93487600-93500000	Strong transcription	Brain Angular Gyrus	brain
5	chr15:93491600-93498400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:93493000-93500400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:93493000-93508600	Strong transcription	Hela-S3	cervix
8	chr15:93493200-93499800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:93493200-93503800	Strong transcription	Brain Substantia Nigra	brain
10	chr15:93493200-93504400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:93493200-93504800	Strong transcription	Fetal Kidney	kidney
12	chr15:93493200-93508200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:93493200-93512200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:93493200-93533000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:93493200-93536000	Strong transcription	HSMM	muscle
16	chr15:93493200-93571000	Strong transcription	Dnd41	blood
17	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr15:93493400-93498200	Strong transcription	Fetal Stomach	stomach
19	chr15:93493400-93500400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:93493400-93500400	Strong transcription	NHDF-Ad	bronchial
21	chr15:93493400-93500600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:93493400-93500600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:93493400-93500600	Strong transcription	NH-A	brain
24	chr15:93493400-93501400	Strong transcription	HSMMtube	muscle
25	chr15:93493400-93501600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:93493400-93501600	Strong transcription	Brain Hippocampus Middle	brain
27	chr15:93493400-93501800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:93493400-93503000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:93493400-93504800	Strong transcription	Brain Anterior Caudate	brain
30	chr15:93493400-93505000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr15:93493400-93505800	Strong transcription	Fetal Lung	lung
32	chr15:93493400-93508200	Strong transcription	Primary B cells from cord blood	blood
33	chr15:93493400-93508400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:93493400-93511800	Strong transcription	Adipose Nuclei	Adipose
35	chr15:93493400-93511800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr15:93493400-93568600	Strong transcription	Liver	Liver
38	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
39	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:93493600-93501000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr15:93493600-93504800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr15:93493600-93510600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:93493600-93521600	Strong transcription	Osteobl	bone
45	chr15:93493600-93523400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:93493600-93571400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:93493800-93498400	Strong transcription	Lung	lung
48	chr15:93493800-93500400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:93493800-93501600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:93493800-93502600	Strong transcription	NHLF	lung

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