Variant report

Variant	rs10744729
Chromosome Location	chr12:1024594-1024595
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:1024370-1024710	HepG2	liver:	n/a	n/a
2	SPI1	chr12:1024222-1024771	HL-60	blood:	n/a	n/a
3	POLR2A	chr12:1024034-1024852	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr12:1021919-1024830	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:1024058-1024840	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr12:1021154-1024803	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:1020572-1024907	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:1022632-1024767	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:1021206-1024874	A549	lung:	n/a	n/a
10	POLR2A	chr12:1024036-1024857	GM12891	blood:	n/a	n/a
11	POLR2A	chr12:1024554-1024709	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:1024559-1024699	K562	blood:	n/a	n/a
13	POLR2A	chr12:1024067-1024800	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr12:1024148-1024658	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:1024251-1024600	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:1024582-1024932	MCF-7	breast:	n/a	n/a
17	POLR2A	chr12:1021945-1024849	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1014162..1017622-chr12:1021413..1026114,4	K562	blood:

Variant related genes	Relation type
RAD52	TF binding region
ENSG00000060237	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10849578	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849579	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10849584	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064580	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11064585	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11064593	0.97[ASN][1000 genomes]
rs11226	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11571409	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11571448	0.95[ASN][1000 genomes]
rs11611051	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11614499	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12581940	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255390	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2269937	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286029	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748521	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4766370	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4980974	0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6413436	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.97[ASN][1000 genomes]
rs7296555	0.94[ASN][1000 genomes]
rs7300444	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7300718	0.97[ASN][1000 genomes]
rs7301931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303748	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7308979	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7310449	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962050	0.80[YRI][hapmap]
rs7964502	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953361	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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 target site	80 gene(s)	inside rSNPs	diseases
3	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
10	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1042333	chr12:907975-1081509	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
15	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	nsv1053198	chr12:993822-1034603	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
20	nsv541341	chr12:993822-1034603	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
21	nsv1041675	chr12:993822-1091354	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
22	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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
23	nsv492321	chr12:1011692-1388512	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
24	nsv898579	chr12:1013176-1510505	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10744729	RAD52	cis	cerebellum	SCAN
rs10744729	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:964400-1042200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:964600-1027200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:965800-1028400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:982200-1027000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:986200-1042200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:986800-1028400	Strong transcription	Placenta	Placenta
7	chr12:987000-1028400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:987000-1028800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:987000-1041200	Strong transcription	Fetal Intestine Large	intestine
10	chr12:988600-1029400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:989200-1042200	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:989400-1028400	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:995200-1025800	Weak transcription	Stomach Mucosa	stomach
14	chr12:1001800-1028200	Strong transcription	HepG2	liver
15	chr12:1003400-1024600	Strong transcription	HMEC	breast
16	chr12:1003600-1028000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:1003600-1028200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr12:1003600-1028400	Strong transcription	NHDF-Ad	bronchial
19	chr12:1004200-1027200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:1004400-1041200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:1004800-1037400	Strong transcription	Fetal Lung	lung
22	chr12:1005000-1028000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:1005200-1028800	Strong transcription	Rectal Smooth Muscle	rectum
24	chr12:1006000-1026400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:1006600-1028200	Strong transcription	HSMMtube	muscle
26	chr12:1007000-1028400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:1008000-1028000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:1008200-1026600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr12:1008200-1028800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:1008800-1025800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr12:1009400-1026600	Strong transcription	Brain Germinal Matrix	brain
32	chr12:1009400-1027200	Strong transcription	Colonic Mucosa	Colon
33	chr12:1013000-1025400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:1013400-1026600	Strong transcription	Liver	Liver
35	chr12:1014200-1026600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr12:1014600-1028200	Strong transcription	Primary T cells from cord blood	blood
37	chr12:1015200-1025600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:1015200-1028000	Strong transcription	Brain Cingulate Gyrus	brain
39	chr12:1015200-1028200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:1015200-1028400	Strong transcription	GM12878-XiMat	blood
41	chr12:1015200-1029200	Strong transcription	Brain Anterior Caudate	brain
42	chr12:1015200-1038800	Weak transcription	Fetal Brain Male	brain
43	chr12:1015400-1028400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr12:1015600-1030800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr12:1015800-1028600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:1016400-1026600	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr12:1017400-1025400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:1017800-1025200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:1019200-1024800	Weak transcription	Small Intestine	intestine
50	chr12:1019200-1028200	Strong transcription	A549	lung

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