Variant report

Variant	rs2607540
Chromosome Location	chr10:28601993-28601994
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	chr10:28590955..28592779-chr10:28600546..28603344,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1004270	0.99[ASN][1000 genomes]
rs10763654	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs10763655	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs10763658	0.84[ASN][1000 genomes]
rs10763659	0.99[ASN][1000 genomes]
rs10826435	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs10826448	0.88[ASN][1000 genomes]
rs10826449	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10826450	0.98[ASN][1000 genomes]
rs11006957	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs11006965	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11006970	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11007007	0.99[ASN][1000 genomes]
rs11007008	0.99[ASN][1000 genomes]
rs11007017	0.81[ASN][1000 genomes]
rs1144513	0.82[ASN][1000 genomes]
rs1144514	0.99[ASN][1000 genomes]
rs1148175	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12221389	0.99[ASN][1000 genomes]
rs12221390	0.99[ASN][1000 genomes]
rs12256403	0.82[CHB][hapmap]
rs1249420	1.00[ASN][1000 genomes]
rs1418757	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1418759	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs17758855	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1870097	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs1870098	0.86[CHB][hapmap]
rs2100615	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2368307	0.99[ASN][1000 genomes]
rs3847388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs60705071	0.99[ASN][1000 genomes]
rs6481515	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7088465	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs7905490	0.82[CHB][hapmap]
rs7913970	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9919403	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1044938	chr10:28601993-28659440	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2607540	GAD2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28592800-28606600	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:28593000-28607600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:28593200-28603000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr10:28593200-28605800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr10:28593200-28615400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:28593400-28613400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr10:28593400-28615200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:28594000-28606600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr10:28596800-28618800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr10:28597200-28605400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:28597200-28611000	Weak transcription	Pancreas	Pancrea
12	chr10:28597400-28606200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr10:28597400-28614000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr10:28597600-28613800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:28600800-28602000	Strong transcription	Primary T cells from cord blood	blood
16	chr10:28601200-28602000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr10:28601400-28602000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:28601400-28602000	Enhancers	NHDF-Ad	bronchial
19	chr10:28601400-28602000	Enhancers	Osteobl	bone
20	chr10:28601600-28615400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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