Variant report

Variant	rs2958127
Chromosome Location	chr12:57114307-57114308
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57113954-57114976	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:57111849-57115834	K562	blood:	n/a	n/a
3	POLR2A	chr12:57113975-57114368	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:57113929-57115771	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:57109373-57115069	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:57114185-57114420	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr12:57109486-57115298	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:57109177-57115890	PFSK-1	brain:	n/a	n/a
9	TEAD4	chr12:57113982-57114609	K562	blood:	n/a	n/a
10	POLR2A	chr12:57112257-57114921	A549	lung:	n/a	n/a
11	POLR2A	chr12:57113675-57114456	U87	brain:	n/a	n/a
12	POLR2A	chr12:57112532-57115744	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr12:57114086-57114725	GM12891	blood:	n/a	n/a
14	POLR2A	chr12:57109283-57116293	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:57114280-57115427	K562	blood:	n/a	n/a
16	POLR2A	chr12:57114268-57114707	ECC-1	luminal epithelium:	n/a	n/a
17	JUND	chr12:57114228-57114358	K562	blood:	n/a	n/a
18	POLR2A	chr12:57114072-57115772	GM12892	blood:	n/a	n/a
19	POLR2A	chr12:57112634-57115751	K562	blood:	n/a	n/a
20	POLR2A	chr12:57113751-57115655	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:57113730-57114401	U87	brain:	n/a	n/a
22	POLR2A	chr12:57109094-57117058	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr12:57113735-57114437	U87	brain:	n/a	n/a
24	POLR2A	chr12:57114094-57116142	K562	blood:	n/a	n/a
25	POLR2A	chr12:57112872-57115428	HL-60	blood:	n/a	n/a
26	POLR2A	chr12:57113873-57114675	K562	blood:	n/a	n/a
27	POLR2A	chr12:57109356-57117115	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:57114108-57114467	HCT-116	colon:	n/a	n/a
29	POLR2A	chr12:57114195-57114378	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:57112599-57115857	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:57113802-57114403	GM12891	blood:	n/a	n/a
32	POLR2A	chr12:57109233-57116354	PANC-1	pancreas:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57075341..57085478-chr12:57112447..57121011,58	MCF-7	breast:
2	chr12:57113156..57115169-chr12:57146013..57147663,2	K562	blood:
3	chr12:57113713..57116326-chr12:57145534..57147437,2	MCF-7	breast:
4	chr12:57038025..57041646-chr12:57113711..57120620,12	MCF-7	breast:
5	chr12:57074578..57085543-chr12:57108746..57121559,55	K562	blood:
6	chr12:57091435..57092961-chr12:57113686..57115355,2	K562	blood:
7	chr12:57076604..57085974-chr12:57112559..57120474,46	MCF-7	breast:
8	chr12:57078475..57085183-chr12:57112918..57121559,38	K562	blood:
9	chr12:57022951..57032187-chr12:57113330..57121462,17	K562	blood:
10	chr12:57113663..57115512-chr12:57124278..57127097,2	K562	blood:

No data

Variant related genes	Relation type
NACA	TF binding region
ENSG00000025423	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000110955	Chromatin interaction
ENSG00000207031	Chromatin interaction
ENSG00000196531	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1026565	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459246	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747769	0.83[EUR][1000 genomes]
rs10747770	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783796	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876916	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876918	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107479	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs11171914	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs11171951	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171956	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171986	0.81[JPT][hapmap]
rs1131514	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12227117	0.82[ASN][1000 genomes]
rs12229457	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs12828563	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466382	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563896	0.85[CEU][hapmap];0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs1563897	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1975875	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1979325	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2035081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035082	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255074	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs2290893	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2926743	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2926747	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2926748	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950387	0.80[CHB][hapmap];0.86[TSI][hapmap]
rs2950390	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2958123	0.95[CEU][hapmap];0.93[CHB][hapmap]
rs2958130	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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958132	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958134	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958148	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2958149	0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2958153	0.93[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2958154	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2958155	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs3214051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4277148	0.81[JPT][hapmap]
rs4759254	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs4759256	0.90[ASN][1000 genomes]
rs4788	0.96[ASN][1000 genomes]
rs4902	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137749	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7295862	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7297289	0.80[ASN][1000 genomes]
rs7303216	0.80[ASN][1000 genomes]
rs7313074	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7966391	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967600	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];0.93[MKK][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978685	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7980317	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];0.97[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7980835	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs898609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs941207	0.86[CHB][hapmap]
rs9634246	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs9989034	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv20867	chr12:57110564-57115506	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2958127	MUCL1	cis	parietal	SCAN
rs2958127	PRIM1	cis	parietal	SCAN
rs2958127	RBMS2	cis	multi-tissue	Pritchard
rs2958127	CELA1	cis	cerebellum	SCAN
rs2958127	RAB5B	cis	cerebellum	SCAN
rs2958127	HSD17B6	cis	cerebellum	SCAN
rs2958127	PRIM1	cis	cerebellum	SCAN
rs2958127	OR6C4	cis	cerebellum	SCAN
rs2958127	PRIM1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57104000-57114600	Weak transcription	Fetal Brain Male	brain
2	chr12:57104600-57115000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:57108400-57115400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:57108600-57117200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:57109200-57116200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:57109400-57114800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:57109600-57115400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
8	chr12:57109600-57116000	Genic enhancers	Fetal Muscle Leg	muscle
9	chr12:57109600-57117000	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr12:57109600-57117000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr12:57109600-57117800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:57109800-57114400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:57109800-57114600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr12:57109800-57115800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr12:57109800-57117200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:57110200-57115400	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr12:57110200-57115800	Genic enhancers	Placenta	Placenta
18	chr12:57110200-57116800	Genic enhancers	Fetal Stomach	stomach
19	chr12:57110400-57116800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:57110400-57117600	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr12:57110800-57114600	Weak transcription	Ovary	ovary
22	chr12:57111200-57114800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:57111200-57114800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:57111200-57114800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:57111400-57114800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:57112000-57115400	Genic enhancers	A549	lung
27	chr12:57112000-57115600	Genic enhancers	Lung	lung
28	chr12:57112000-57116000	Genic enhancers	Fetal Intestine Small	intestine
29	chr12:57112200-57115800	Enhancers	Fetal Heart	heart
30	chr12:57112200-57117000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:57112200-57117200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:57112400-57114400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:57112400-57114600	Genic enhancers	Fetal Lung	lung
34	chr12:57112400-57114800	Genic enhancers	Psoas Muscle	Psoas
35	chr12:57112400-57114800	Enhancers	Right Atrium	heart
36	chr12:57112400-57114800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:57112400-57115000	Genic enhancers	Brain Hippocampus Middle	brain
38	chr12:57112400-57115000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr12:57112400-57115800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr12:57112400-57116800	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:57112600-57114400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:57112600-57114400	Strong transcription	HUVEC	blood vessel
43	chr12:57112600-57114600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:57112600-57114600	Genic enhancers	Duodenum Mucosa	Duodenum
45	chr12:57112600-57114600	Strong transcription	HSMM	muscle
46	chr12:57112600-57114800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
47	chr12:57112600-57114800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr12:57112600-57114800	Strong transcription	Aorta	Aorta
49	chr12:57112600-57114800	Genic enhancers	Dnd41	blood
50	chr12:57112600-57114800	Strong transcription	HSMMtube	muscle

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