Variant report

Variant	rs2290894
Chromosome Location	chr12:57108695-57108696
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57108132-57109042	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr12:57108230-57108814	A549	lung:	n/a	n/a
3	POLR2A	chr12:57106213-57109097	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:57108612-57109074	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:57108445-57108973	U87	brain:	n/a	n/a
6	POLR2A	chr12:57108497-57108888	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:57108428-57108709	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:57108659-57108968	K562	blood:	n/a	n/a
9	POLR2A	chr12:57107991-57108696	MCF-7	breast:	n/a	n/a
10	POLR2A	chr12:57108563-57108716	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:57108237-57108900	K562	blood:	n/a	n/a
12	POLR2A	chr12:57108026-57111457	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:57108491-57108973	U87	brain:	n/a	n/a
14	POLR2A	chr12:57106181-57108985	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr12:57106765-57109180	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57106579..57108709-chrX:20158606..20161019,2	K562	blood:
2	chr12:57078008..57083064-chr12:57107591..57112002,6	MCF-7	breast:
3	chr12:57079048..57083970-chr12:57107938..57112602,6	K562	blood:

No data

Variant related genes	Relation type
NACA	TF binding region
ENSG00000173674	Chromatin interaction
ENSG00000110958	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1026565	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459246	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747769	0.83[EUR][1000 genomes]
rs10747770	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783796	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876916	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876918	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107479	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[YRI][hapmap]
rs11171914	0.91[CEU][hapmap];0.93[CHB][hapmap]
rs11171951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171956	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171986	0.82[JPT][hapmap]
rs1131514	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12227117	0.82[ASN][1000 genomes]
rs12229457	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs12828563	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466382	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563896	0.86[CEU][hapmap];0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs1563897	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1975875	0.94[AFR][1000 genomes];1.00[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[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035082	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255074	0.95[CEU][hapmap];0.93[CHB][hapmap]
rs2290893	0.95[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2926741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2926743	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2926747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2926748	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950387	0.80[CHB][hapmap]
rs2950390	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs2958123	0.95[CEU][hapmap];0.94[CHB][hapmap]
rs2958127	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]
rs2958130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958132	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958134	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958148	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2958149	0.93[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2958153	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs2958154	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs2958155	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs3214051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4277148	0.81[JPT][hapmap]
rs4759254	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs4759256	0.90[ASN][1000 genomes]
rs4788	0.96[ASN][1000 genomes]
rs4902	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137749	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7295862	1.00[CEU][hapmap];0.89[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];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7966391	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978685	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7980317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs941207	0.87[CHB][hapmap]
rs9634246	0.93[CHB][hapmap]
rs9989034	0.80[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	nsv559016	chr12:57095815-57112637	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57089000-57109600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:57104000-57114600	Weak transcription	Fetal Brain Male	brain
3	chr12:57104600-57109000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:57104600-57109200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:57104600-57109400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:57104600-57109400	Strong transcription	Lung	lung
7	chr12:57104600-57109800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:57104600-57110200	Strong transcription	Fetal Stomach	stomach
9	chr12:57104600-57112600	Strong transcription	Fetal Intestine Large	intestine
10	chr12:57104600-57115000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:57104800-57109400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:57104800-57109600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:57104800-57109600	Strong transcription	Liver	Liver
14	chr12:57104800-57109600	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:57104800-57109600	Strong transcription	NH-A	brain
16	chr12:57104800-57109800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:57104800-57109800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr12:57104800-57110000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:57104800-57110000	Strong transcription	Brain Germinal Matrix	brain
20	chr12:57104800-57110000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr12:57104800-57110000	Strong transcription	A549	lung
22	chr12:57104800-57110200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:57104800-57110200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:57104800-57110200	Strong transcription	Placenta	Placenta
25	chr12:57104800-57110400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:57104800-57110600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:57104800-57110600	Strong transcription	Osteobl	bone
28	chr12:57104800-57111000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:57104800-57111200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:57104800-57111200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:57104800-57111200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:57104800-57111200	Strong transcription	HSMM	muscle
33	chr12:57104800-57111400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:57105000-57108800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:57105000-57109000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:57105000-57109000	Strong transcription	Brain Substantia Nigra	brain
37	chr12:57105000-57109400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:57105000-57109600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:57105000-57109600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:57105000-57109600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:57105000-57109600	Strong transcription	Adipose Nuclei	Adipose
42	chr12:57105000-57109600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:57105000-57109600	Strong transcription	HUVEC	blood vessel
44	chr12:57105000-57109800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:57105000-57109800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:57105000-57109800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr12:57105000-57110000	Strong transcription	Primary B cells from cord blood	blood
48	chr12:57105000-57110200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr12:57105000-57110200	Strong transcription	Dnd41	blood
50	chr12:57105000-57110400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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