Variant report

Variant	rs6489056
Chromosome Location	chr12:122999535-122999536
allele	C/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	chr12:122999515-123001085	K562	blood:	n/a	n/a
2	POLR2A	chr12:122999444-123002873	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:122999362-123000472	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:122999515-123000278	K562	blood:	n/a	n/a
5	POLR2A	chr12:122999495-122999792	GM12891	blood:	n/a	n/a
6	POLR2A	chr12:122999423-123000428	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:122999490-123000276	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:122999508-123000181	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:122999492-123000559	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:122999521-123000540	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:122999489-123000157	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:122999495-123000593	GM12892	blood:	n/a	n/a
13	POLR2A	chr12:122999487-123000250	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122992391..122995677-chr12:122999223..123001586,3	MCF-7	breast:

Variant related genes	Relation type
RSRC2	TF binding region
ENSG00000111011	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10744242	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773117	0.87[GIH][hapmap]
rs10773230	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10846714	0.81[GIH][hapmap]
rs10846912	1.00[JPT][hapmap]
rs10846968	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs10847090	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058362	0.88[EUR][1000 genomes]
rs11058398	0.88[EUR][1000 genomes]
rs11058562	0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs11610303	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11611668	0.82[CHD][hapmap]
rs11615830	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12371048	0.88[EUR][1000 genomes]
rs12812332	0.95[JPT][hapmap]
rs12817342	0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs12825762	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12828165	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1392142	0.87[GIH][hapmap]
rs1532578	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1532579	0.87[GIH][hapmap]
rs2133557	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4356269	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4758657	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs4758658	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs4758660	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4758692	0.88[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57311174	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58600355	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61956119	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61956121	0.83[ASN][1000 genomes]
rs6416295	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs6488947	0.87[GIH][hapmap]
rs6489014	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs6489051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132830	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7134381	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136564	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7296680	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs7297866	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298839	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7303688	0.87[EUR][1000 genomes]
rs7307867	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311573	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs7486949	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7955513	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs7961258	0.87[GIH][hapmap]
rs7967928	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7974160	0.81[GIH][hapmap]

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	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122986000-123001800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:122986200-123007600	Weak transcription	Right Atrium	heart
3	chr12:122986400-123003200	Strong transcription	Fetal Stomach	stomach
4	chr12:122986400-123007800	Strong transcription	Placenta	Placenta
5	chr12:122986800-123001800	Strong transcription	Osteobl	bone
6	chr12:122986800-123002000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:122986800-123006600	Strong transcription	Brain Germinal Matrix	brain
8	chr12:122986800-123006800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:122986800-123007000	Strong transcription	Fetal Muscle Leg	muscle
10	chr12:122986800-123009400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:122987000-123007800	Strong transcription	Fetal Thymus	thymus
12	chr12:122987200-123003200	Strong transcription	Fetal Intestine Small	intestine
13	chr12:122987400-123003000	Strong transcription	Lung	lung
14	chr12:122987400-123006800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:122987400-123007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:122987400-123007200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:122987400-123007400	Strong transcription	Thymus	Thymus
18	chr12:122987400-123007600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:122987400-123007800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:122987400-123007800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:122987600-123001000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:122987600-123001800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:122987600-123001800	Strong transcription	NH-A	brain
24	chr12:122987600-123002200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:122987600-123002600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:122987600-123003600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:122987600-123004000	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:122987600-123004600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:122987600-123006000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:122987600-123006400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:122987600-123006400	Strong transcription	Liver	Liver
32	chr12:122987600-123006400	Strong transcription	Brain Hippocampus Middle	brain
33	chr12:122987600-123006600	Strong transcription	Primary T cells from cord blood	blood
34	chr12:122987600-123006800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:122987600-123007000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:122987600-123007000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:122987600-123007000	Strong transcription	Fetal Intestine Large	intestine
38	chr12:122987600-123007000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr12:122987600-123007600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:122987600-123007600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:122987600-123008000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:122987800-123001400	Strong transcription	Left Ventricle	heart
43	chr12:122987800-123001600	Strong transcription	NHLF	lung
44	chr12:122987800-123001800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:122987800-123001800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:122987800-123001800	Strong transcription	HSMM	muscle
47	chr12:122987800-123001800	Strong transcription	HSMMtube	muscle
48	chr12:122987800-123002600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:122987800-123002600	Strong transcription	Dnd41	blood
50	chr12:122987800-123002600	Strong transcription	NHDF-Ad	bronchial

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