Variant report

Variant	rs10787298
Chromosome Location	chr10:112788041-112788042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10787292	0.85[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10885076	0.92[ASW][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs12412661	0.95[EUR][1000 genomes]
rs1327553	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1359849	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1410054	0.90[ASN][1000 genomes]
rs1410055	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1410057	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs1581886	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs17128194	0.81[GIH][hapmap]
rs1887460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980869	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4309090	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6585026	0.92[ASW][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap]
rs6585027	0.85[ASN][1000 genomes]
rs7082572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7085088	0.95[EUR][1000 genomes]
rs7086350	0.85[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs7088364	0.90[ASN][1000 genomes]
rs7090695	0.95[EUR][1000 genomes]
rs7095404	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs7101075	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs990429	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1042020	chr10:112686323-112795159	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1048444	chr10:112724159-112795159	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1051595	chr10:112730022-112789048	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10787298	HABP2	cis	parietal	SCAN
rs10787298	NRAP	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112705200-112789800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:112732600-112789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:112732800-112789400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:112740400-112791800	Weak transcription	Colon Smooth Muscle	Colon
5	chr10:112749200-112789400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:112753400-112789600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr10:112765000-112794200	Weak transcription	NH-A	brain
8	chr10:112765000-112794400	Weak transcription	NHLF	lung
9	chr10:112765200-112794200	Weak transcription	NHEK	skin
10	chr10:112770800-112798800	Weak transcription	HMEC	breast
11	chr10:112772800-112789200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:112773000-112793200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:112773000-112794000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr10:112778600-112789000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:112781000-112794200	Weak transcription	HSMM	muscle
16	chr10:112781400-112788400	Weak transcription	GM12878-XiMat	blood
17	chr10:112782400-112789000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:112783000-112789200	Weak transcription	Fetal Thymus	thymus
19	chr10:112783000-112789400	Weak transcription	Aorta	Aorta
20	chr10:112783000-112789800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr10:112783000-112792600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:112783000-112794200	Weak transcription	Osteobl	bone
23	chr10:112783000-112794400	Weak transcription	HSMMtube	muscle
24	chr10:112783200-112788200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr10:112783200-112788800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr10:112783200-112789400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:112783200-112789600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:112783200-112791600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr10:112783200-112791800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:112783400-112789200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr10:112783400-112789200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr10:112783400-112789400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr10:112783400-112801400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:112783600-112790000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:112783600-112794200	Weak transcription	NHDF-Ad	bronchial
36	chr10:112783800-112788600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr10:112783800-112791600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr10:112783800-112794200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr10:112784000-112789000	Weak transcription	Primary B cells from cord blood	blood
40	chr10:112786800-112788800	Weak transcription	Primary T cells from cord blood	blood
41	chr10:112786800-112789200	Weak transcription	Primary hematopoietic stem cells	blood

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