Variant report

Variant	rs10493860
Chromosome Location	chr1:92212703-92212704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92198271..92200616-chr1:92212506..92214595,2	MCF-7	breast:
2	chr1:92211221..92213860-chr1:92214321..92216295,2	K562	blood:
3	chr1:92195746..92200158-chr1:92212228..92214643,4	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10874925	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11165441	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12121039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121065	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127610	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127644	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12128642	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129174	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133753	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17131550	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28406383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522702	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7526590	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7529421	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9887787	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9887957	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription 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	19 gene(s)	inside rSNPs	diseases
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10493860	TMEM56	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92197000-92215200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:92197200-92215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:92197600-92230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:92198200-92224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:92199200-92218600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:92199400-92219000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:92201200-92219000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:92201400-92217600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:92203200-92212800	Weak transcription	Spleen	Spleen
10	chr1:92204800-92247000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:92206200-92213600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:92208400-92235800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:92208800-92214800	Weak transcription	Brain Substantia Nigra	brain
14	chr1:92209200-92215600	Weak transcription	Osteobl	bone
15	chr1:92209200-92217000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:92209400-92213400	Weak transcription	Psoas Muscle	Psoas
17	chr1:92210400-92213400	Enhancers	Fetal Lung	lung
18	chr1:92210600-92213600	Weak transcription	Right Ventricle	heart
19	chr1:92211000-92215200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:92211000-92215600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:92211200-92213000	ZNF genes & repeats	A549	lung
22	chr1:92211200-92215000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:92211200-92215200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:92211200-92215800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:92211200-92216000	Weak transcription	Aorta	Aorta
26	chr1:92211400-92212800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:92211400-92213000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:92211400-92213000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:92211400-92213600	Enhancers	Liver	Liver
30	chr1:92211400-92215400	Weak transcription	Small Intestine	intestine
31	chr1:92211400-92215800	Weak transcription	Brain Angular Gyrus	brain
32	chr1:92211600-92216200	Weak transcription	Brain Germinal Matrix	brain
33	chr1:92211800-92214800	Weak transcription	Brain Anterior Caudate	brain
34	chr1:92211800-92215400	Weak transcription	Pancreas	Pancrea
35	chr1:92211800-92215600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:92211800-92235600	Weak transcription	Fetal Kidney	kidney
37	chr1:92212000-92213200	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr1:92212000-92214000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:92212000-92214200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:92212000-92215000	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:92212000-92216800	Weak transcription	Fetal Heart	heart
42	chr1:92212200-92213000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:92212400-92212800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:92212400-92212800	ZNF genes & repeats	Adipose Nuclei	Adipose
45	chr1:92212400-92213000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr1:92212400-92213000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:92212400-92213000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
48	chr1:92212400-92213000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:92212400-92213000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:92212400-92213000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet

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