Variant report

Variant	rs2235015
Chromosome Location	chr7:87199564-87199565
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10225473	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs10244266	0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs10268314	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs10274441	0.89[ASN][1000 genomes]
rs10274587	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs10276603	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs10280101	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs10280623	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10808071	0.85[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap]
rs11760837	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs11772987	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11972405	0.83[ASN][1000 genomes]
rs11979702	1.00[JPT][hapmap]
rs11983225	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs1202171	0.88[JPT][hapmap]
rs1202175	0.88[JPT][hapmap]
rs1202180	0.84[GIH][hapmap];0.88[JPT][hapmap]
rs1202181	0.88[JPT][hapmap]
rs1202182	0.88[JPT][hapmap]
rs1202185	0.88[JPT][hapmap]
rs1202186	0.88[JPT][hapmap]
rs12334183	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12720067	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs1882479	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1989830	0.88[JPT][hapmap]
rs2032583	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs2235040	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs2235067	0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs28718458	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148739	0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs4148740	1.00[JPT][hapmap]
rs60412009	0.86[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	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1026153	chr7:86905796-87258822	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2235015	GTPBP10	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87139400-87211000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr7:87144600-87215600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr7:87146200-87228000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:87174600-87219800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:87179600-87212800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:87195400-87200400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:87196000-87211200	Weak transcription	Primary T cells from cord blood	blood
8	chr7:87196600-87213000	Weak transcription	Placenta	Placenta
9	chr7:87196800-87208400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:87197000-87200000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:87197000-87200400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr7:87197800-87199600	Enhancers	Fetal Intestine Small	intestine
13	chr7:87197800-87200200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr7:87198200-87201800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:87198200-87208600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:87198600-87199800	Enhancers	Fetal Intestine Large	intestine
17	chr7:87198600-87205000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:87199000-87199600	Enhancers	Liver	Liver
19	chr7:87199000-87200600	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr7:87199000-87201200	Enhancers	HepG2	liver
21	chr7:87199200-87199600	Enhancers	HMEC	breast
22	chr7:87199200-87200200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr7:87199200-87200600	Enhancers	NH-A	brain
24	chr7:87199200-87220200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr7:87199200-87228000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:87199400-87200200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:87199400-87200200	Enhancers	NHEK	skin
28	chr7:87199400-87200600	Enhancers	NHLF	lung

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