Variant report

Variant	rs10774594
Chromosome Location	chr12:121842720-121842721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:121842463-121843346	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:121842587-121842787	MCF10A-Er-Src	breast:	n/a	n/a
3	NFIC	chr12:121842505-121842961	HepG2	liver:	n/a	n/a
4	NFIC	chr12:121842398-121843166	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:121842560-121842904	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr12:121842417-121843132	ECC-1	luminal epithelium:	n/a	n/a
7	EP300	chr12:121842555-121842944	SK-N-SH_RA	brain:	n/a	n/a
8	ARID3A	chr12:121842662-121842835	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:121842543-121843469	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:121842618-121842869	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:121842587-121842895	SK-N-MC	brain:	n/a	n/a
12	EP300	chr12:121842582-121842896	SK-N-SH_RA	brain:	n/a	n/a
13	MYC	chr12:121842640-121842863	K562	blood:	n/a	n/a
14	MXI1	chr12:121842673-121842896	HepG2	liver:	n/a	n/a
15	NFIC	chr12:121842543-121842912	SK-N-SH	brain:	n/a	n/a
16	NFIC	chr12:121842383-121843229	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr12:121842597-121843334	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121840334..121842977-chr12:121859647..121861794,2	MCF-7	breast:
2	chr12:121841412..121843273-chr12:121861123..121863390,2	K562	blood:
3	chr12:121842475..121844686-chr12:121864287..121866762,2	MCF-7	breast:
4	chr12:121790056..121793007-chr12:121841274..121843230,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNF34	TF binding region
ENSG00000089053	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10444489	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444491	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10444492	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1064951	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744763	0.96[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs10744764	0.96[CEU][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10774595	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774596	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774597	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10774598	0.96[CEU][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10849873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849875	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849877	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849880	1.00[ASW][hapmap];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[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849882	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849884	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849885	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849887	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10849889	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10849891	0.92[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065549	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065551	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065563	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065565	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065576	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065577	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065578	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065579	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065582	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065583	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065585	0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11838335	0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12427382	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12578785	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12581843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581861	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288154	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28604990	0.86[ASW][hapmap];1.00[YRI][hapmap]
rs28663167	0.86[ASW][hapmap];1.00[YRI][hapmap]
rs3751131	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817543	0.96[CEU][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817544	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817545	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817546	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817547	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3817549	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817551	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4081775	1.00[ASW][hapmap];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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4980986	0.86[ASW][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs4980994	0.86[ASW][hapmap];0.86[CHD][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs57185007	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57889600	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57971979	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58609847	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58849369	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59103597	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59190874	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953461	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61953462	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61953497	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61955092	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61955131	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61955132	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61955138	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9300314	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634167	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634168	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10774594	TAOK3	cis	parietal	SCAN
rs10774594	NME2P1	cis	cerebellum	SCAN
rs10774594	TMEM120B	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121838800-121843000	Weak transcription	Lung	lung
2	chr12:121838800-121852600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:121839000-121842800	Weak transcription	Left Ventricle	heart
4	chr12:121839000-121842800	Weak transcription	Spleen	Spleen
5	chr12:121839000-121852600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:121839000-121853800	Weak transcription	Ovary	ovary
7	chr12:121839000-121854800	Weak transcription	Gastric	stomach
8	chr12:121839000-121855200	Weak transcription	Fetal Brain Male	brain
9	chr12:121839000-121855400	Weak transcription	Aorta	Aorta
10	chr12:121839000-121855400	Weak transcription	Esophagus	oesophagus
11	chr12:121839000-121855400	Weak transcription	Pancreas	Pancrea
12	chr12:121839000-121855400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:121839000-121861000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:121839000-121866400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:121839000-121866400	Weak transcription	Small Intestine	intestine
16	chr12:121839200-121842800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:121839200-121842800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:121839200-121854800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:121839200-121855000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:121839200-121855400	Weak transcription	Right Ventricle	heart
21	chr12:121839200-121855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:121839200-121856800	Weak transcription	HSMMtube	muscle
23	chr12:121839200-121860800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:121839400-121842800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:121839400-121842800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:121839400-121844800	Weak transcription	Colonic Mucosa	Colon
27	chr12:121839600-121842800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:121839600-121854800	Weak transcription	Stomach Mucosa	stomach
29	chr12:121839800-121842800	Weak transcription	Fetal Kidney	kidney
30	chr12:121839800-121844400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:121839800-121855200	Weak transcription	Brain Angular Gyrus	brain
32	chr12:121840000-121842800	Weak transcription	Primary B cells from cord blood	blood
33	chr12:121840000-121842800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:121840000-121843000	Weak transcription	Fetal Brain Female	brain
35	chr12:121840000-121844200	Weak transcription	Brain Substantia Nigra	brain
36	chr12:121840000-121855200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:121840200-121844000	Weak transcription	Liver	Liver
38	chr12:121840400-121846600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:121840400-121847800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:121840400-121852000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:121840600-121842800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:121840600-121847600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:121840600-121847800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:121840600-121848800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:121840600-121855000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:121840800-121842800	Weak transcription	K562	blood
47	chr12:121840800-121844400	Weak transcription	Primary T cells from cord blood	blood
48	chr12:121840800-121846000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:121840800-121847000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:121840800-121847400	Strong transcription	Rectal Mucosa Donor 29	rectum

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