Variant report

Variant	rs12742961
Chromosome Location	chr1:169794862-169794863
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10489172	0.90[ASW][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1062976	0.90[ASW][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10919246	0.83[ASW][hapmap];0.96[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10919250	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10919252	0.95[CEU][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10919255	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10919256	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919258	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919259	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576078	0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12059182	0.83[YRI][hapmap]
rs12064636	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12089057	0.83[CEU][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs12405525	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760399	0.90[ASW][hapmap];0.94[LWK][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17529513	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17603022	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2205846	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223286	0.85[JPT][hapmap]
rs2272917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2272918	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790399	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3817858	0.93[ASN][1000 genomes]
rs3917458	1.00[JPT][hapmap]
rs3917460	1.00[JPT][hapmap]
rs4987353	0.85[JPT][hapmap]
rs4987367	0.85[JPT][hapmap]
rs4987369	0.85[JPT][hapmap]
rs4987396	1.00[JPT][hapmap]
rs5355	1.00[JPT][hapmap]
rs648576	0.86[MEX][hapmap]
rs6694855	0.80[AFR][1000 genomes]
rs67274208	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026213	0.80[AFR][1000 genomes]
rs73026223	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers 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	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12742961	C1orf112	cis	parietal	SCAN
rs12742961	SELL	cis	multi-tissue	Pritchard
rs12742961	C1orf112	Cis_1M	lymphoblastoid	RTeQTL
rs12742961	MPZL1	cis	parietal	SCAN
rs12742961	SCYL3	cis	parietal	SCAN
rs12742961	C1orf112	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169795200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:169764800-169796200	Weak transcription	Spleen	Spleen
3	chr1:169764800-169818200	Weak transcription	Esophagus	oesophagus
4	chr1:169764800-169818200	Weak transcription	Lung	lung
5	chr1:169764800-169823600	Weak transcription	Gastric	stomach
6	chr1:169765000-169808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:169765200-169797400	Weak transcription	HSMMtube	muscle
9	chr1:169765200-169802000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:169765200-169807800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:169765200-169808000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:169765200-169809000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:169765200-169814800	Weak transcription	Brain Anterior Caudate	brain
14	chr1:169765200-169815200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:169765200-169818800	Weak transcription	Brain Angular Gyrus	brain
16	chr1:169765200-169820600	Weak transcription	Psoas Muscle	Psoas
17	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
18	chr1:169765400-169796800	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:169765400-169798400	Weak transcription	Brain Germinal Matrix	brain
20	chr1:169765400-169798400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:169765400-169808000	Weak transcription	Fetal Heart	heart
22	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
23	chr1:169765600-169808000	Weak transcription	Small Intestine	intestine
24	chr1:169765600-169818200	Weak transcription	NHLF	lung
25	chr1:169765800-169808000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:169765800-169815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:169765800-169818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:169766000-169796800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:169766000-169797000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:169766000-169797400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:169773400-169796200	Weak transcription	HMEC	breast
32	chr1:169773400-169798400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:169773400-169808000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:169773800-169796200	Weak transcription	NH-A	brain
35	chr1:169773800-169796200	Weak transcription	Osteobl	bone
36	chr1:169774800-169796200	Weak transcription	HUVEC	blood vessel
37	chr1:169774800-169796400	Weak transcription	Fetal Intestine Large	intestine
38	chr1:169774800-169800800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:169776200-169796000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:169776400-169808000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr1:169777200-169797800	Weak transcription	Fetal Brain Female	brain
42	chr1:169777200-169798600	Weak transcription	Hela-S3	cervix
43	chr1:169777400-169796600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:169777400-169815400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:169782800-169799800	Weak transcription	NHDF-Ad	bronchial
46	chr1:169784000-169814000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:169784000-169814800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:169785000-169796200	Weak transcription	Ovary	ovary
49	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:169786400-169801400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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