Variant report

Variant	rs1148178
Chromosome Location	chr10:28615573-28615574
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11006935	0.82[CHB][hapmap]
rs11006941	0.82[CHB][hapmap]
rs11006942	0.82[CHB][hapmap]
rs1148177	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148179	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148180	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148181	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1148185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148187	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1148189	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12098315	1.00[ASN][1000 genomes]
rs12098711	0.82[ASN][1000 genomes]
rs12098714	0.86[ASN][1000 genomes]
rs12098807	1.00[ASN][1000 genomes]
rs12254745	0.82[CHB][hapmap]
rs1249340	0.89[ASN][1000 genomes]
rs1249347	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1273097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379320	0.82[ASN][1000 genomes]
rs16928633	0.82[CHB][hapmap]
rs1762188	0.90[ASN][1000 genomes]
rs2100614	1.00[CHB][hapmap]
rs2447629	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2995539	0.82[ASN][1000 genomes]
rs34827546	1.00[ASN][1000 genomes]
rs61845947	0.90[ASN][1000 genomes]
rs7078271	0.82[CHB][hapmap]
rs7100335	0.82[CHB][hapmap]
rs72803699	0.96[ASN][1000 genomes]
rs72805609	0.96[ASN][1000 genomes]
rs72805627	1.00[ASN][1000 genomes]
rs72805630	0.93[ASN][1000 genomes]
rs72805631	0.89[ASN][1000 genomes]
rs7898888	1.00[JPT][hapmap]
rs7911615	0.82[CHB][hapmap]
rs7916525	0.82[CHB][hapmap]
rs811496	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs813081	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs1148178	ARHGAP12	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28596800-28618800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr10:28604000-28615600	Weak transcription	Primary T cells from cord blood	blood
3	chr10:28607000-28615600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:28609200-28615600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:28609200-28615800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr10:28611800-28615600	Weak transcription	Pancreas	Pancrea
7	chr10:28614000-28619000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr10:28614400-28615800	Enhancers	Fetal Muscle Leg	muscle
9	chr10:28614600-28617800	Enhancers	Fetal Stomach	stomach
10	chr10:28614800-28617000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr10:28614800-28620600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:28615000-28615600	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr10:28615000-28616200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:28615000-28617000	Enhancers	Primary hematopoietic stem cells	blood
15	chr10:28615000-28617000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr10:28615000-28620000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr10:28615200-28615600	Enhancers	Brain Angular Gyrus	brain
18	chr10:28615200-28615600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr10:28615200-28615600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr10:28615200-28615600	Enhancers	Psoas Muscle	Psoas
21	chr10:28615200-28615600	Enhancers	Right Atrium	heart
22	chr10:28615200-28615600	Enhancers	HSMMtube	muscle
23	chr10:28615200-28615800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:28615200-28615800	Bivalent Enhancer	Fetal Brain Male	brain
25	chr10:28615200-28615800	Flanking Active TSS	Fetal Heart	heart
26	chr10:28615200-28616000	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr10:28615200-28616000	Enhancers	Fetal Lung	lung
28	chr10:28615200-28616000	Enhancers	Left Ventricle	heart
29	chr10:28615200-28616000	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr10:28615200-28616200	Enhancers	Fetal Thymus	thymus
31	chr10:28615200-28616200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr10:28615200-28616800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:28615200-28616800	Enhancers	Primary B cells from cord blood	blood
34	chr10:28615200-28616800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr10:28615200-28616800	Enhancers	Esophagus	oesophagus
36	chr10:28615200-28617000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr10:28615200-28617000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr10:28615200-28617000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:28615200-28617000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr10:28615200-28617000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr10:28615200-28617200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr10:28615200-28617400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:28615200-28619200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr10:28615200-28621000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:28615400-28615600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:28615400-28615600	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr10:28615400-28615600	Active TSS	Brain Anterior Caudate	brain
48	chr10:28615400-28615600	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr10:28615400-28615600	Enhancers	HSMM	muscle
50	chr10:28615400-28615800	Enhancers	Small Intestine	intestine

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