Variant report

Variant	rs10861407
Chromosome Location	chr12:105758240-105758241
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	chr12:105740078..105742393-chr12:105756994..105759086,2	MCF-7	breast:
2	chr12:105752392..105754695-chr12:105757650..105760428,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10507190	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10861371	1.00[CHB][hapmap]
rs10861400	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10861403	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861411	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861412	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861413	0.98[EUR][1000 genomes]
rs11112434	1.00[CHB][hapmap]
rs11112469	0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs11112470	0.81[EUR][1000 genomes]
rs11112473	0.80[EUR][1000 genomes]
rs11112475	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112478	0.82[EUR][1000 genomes]
rs11112480	0.82[EUR][1000 genomes]
rs11112482	0.94[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs11112483	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112484	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112485	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112486	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112487	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112488	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112492	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112493	1.00[EUR][1000 genomes]
rs11112494	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112495	0.98[EUR][1000 genomes]
rs11112496	0.98[EUR][1000 genomes]
rs11112497	0.98[EUR][1000 genomes]
rs11112498	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11112499	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs11112502	0.98[EUR][1000 genomes]
rs11112504	0.94[EUR][1000 genomes]
rs11112505	0.94[EUR][1000 genomes]
rs11112506	0.94[EUR][1000 genomes]
rs1196748	1.00[CHB][hapmap]
rs1196749	1.00[CHB][hapmap]
rs1196753	1.00[CHB][hapmap]
rs1196754	1.00[CHB][hapmap]
rs1196755	1.00[ASN][1000 genomes]
rs1196756	1.00[CHB][hapmap]
rs1196760	1.00[CHB][hapmap]
rs1196763	1.00[ASN][1000 genomes]
rs1196777	1.00[CHB][hapmap]
rs1196793	1.00[CHB][hapmap]
rs1196852	1.00[CHB][hapmap]
rs1196861	1.00[CHB][hapmap]
rs1196862	1.00[CHB][hapmap]
rs1196864	1.00[CHB][hapmap]
rs12371845	0.98[EUR][1000 genomes]
rs12819965	0.94[EUR][1000 genomes]
rs12820423	0.94[EUR][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs12829692	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12829741	0.98[EUR][1000 genomes]
rs12831150	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1432592	0.81[EUR][1000 genomes]
rs17036960	0.82[EUR][1000 genomes]
rs17041538	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2440715	1.00[CHB][hapmap]
rs2888846	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34346262	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35335704	0.81[EUR][1000 genomes]
rs35519603	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545651	1.00[CHB][hapmap]
rs6797	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7131942	1.00[EUR][1000 genomes]
rs7299225	1.00[CHB][hapmap]
rs7302174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181878	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73181886	1.00[ASN][1000 genomes]
rs7954485	0.81[EUR][1000 genomes]
rs7959385	1.00[CHB][hapmap]
rs7968892	0.98[EUR][1000 genomes]
rs7969370	0.98[EUR][1000 genomes]
rs7969665	0.98[EUR][1000 genomes]
rs7972183	0.81[EUR][1000 genomes]
rs935240	1.00[CHB][hapmap]
rs935241	1.00[CHB][hapmap]
rs935244	1.00[CHB][hapmap]
rs9645790	0.87[EUR][1000 genomes]
rs9645791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899500	chr12:105742674-105803028	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861407	C12orf75	cis	Artery Tibial	GTEx
rs10861407	C12orf75	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105734800-105776600	Weak transcription	Esophagus	oesophagus
2	chr12:105735000-105776600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:105735600-105766800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:105735600-105776600	Weak transcription	Fetal Intestine Small	intestine
5	chr12:105746000-105776800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:105747000-105762000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:105747000-105772600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:105747000-105773200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:105747200-105761400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:105747200-105766000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:105747400-105761800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:105747400-105762000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:105748000-105776600	Weak transcription	Gastric	stomach
14	chr12:105748800-105776800	Weak transcription	Pancreas	Pancrea
15	chr12:105749600-105762600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:105749600-105763800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:105749800-105758600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:105749800-105765600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:105750000-105762600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:105751000-105769000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:105751200-105759600	Weak transcription	HUVEC	blood vessel
22	chr12:105751200-105766200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:105751200-105776800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:105751400-105762600	Weak transcription	HSMMtube	muscle
25	chr12:105751400-105775200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:105751800-105759000	Weak transcription	HMEC	breast
27	chr12:105752000-105762400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:105752200-105765000	Weak transcription	Stomach Mucosa	stomach
29	chr12:105752400-105758400	Strong transcription	NHDF-Ad	bronchial
30	chr12:105752400-105776400	Weak transcription	Aorta	Aorta
31	chr12:105752600-105769000	Strong transcription	Dnd41	blood
32	chr12:105752800-105759200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:105753200-105759200	Weak transcription	Primary B cells from cord blood	blood
34	chr12:105754000-105764200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:105754200-105759000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:105754200-105762000	Weak transcription	GM12878-XiMat	blood
37	chr12:105754200-105763800	Weak transcription	NHEK	skin
38	chr12:105754200-105766400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:105754400-105758800	Weak transcription	Primary T cells from cord blood	blood
40	chr12:105754400-105761600	Weak transcription	NHLF	lung
41	chr12:105754600-105766600	Weak transcription	Fetal Stomach	stomach
42	chr12:105754800-105764000	Weak transcription	Thymus	Thymus
43	chr12:105755400-105759000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:105755400-105759200	Weak transcription	Fetal Brain Male	brain
45	chr12:105755600-105762000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:105755600-105764400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr12:105755800-105758800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:105755800-105759200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:105755800-105759600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:105755800-105760600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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