Variant report

Variant	rs12568279
Chromosome Location	chr1:45312571-45312572
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	chr1:45312564-45313228	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45186339..45188717-chr1:45311854..45313581,2	K562	blood:
2	chr1:45182151..45183755-chr1:45311180..45313361,2	K562	blood:
3	chr1:45312444..45315409-chr1:46048277..46051211,2	K562	blood:
4	chr1:45311178..45313247-chr1:45314183..45316147,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226499	TF binding region
PTCH2	TF binding region
ENSG00000199377	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10158188	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211037	0.96[CEU][hapmap]
rs11211044	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211046	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211047	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11573543	0.84[CHB][hapmap];0.90[ASN][1000 genomes]
rs11577974	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs11584031	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs12059964	0.87[CEU][hapmap];0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs12094007	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120470	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273940	0.92[EUR][1000 genomes]
rs263956	0.87[ASN][1000 genomes]
rs263962	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs263965	0.89[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs263975	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263977	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs264014	0.80[CHB][hapmap]
rs3795720	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][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]
rs6429548	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs6688465	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696675	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698951	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514741	0.90[EUR][1000 genomes]
rs7524446	0.84[CHB][hapmap]
rs7525308	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7526786	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545808	0.92[EUR][1000 genomes]
rs7554177	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs932691	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9645347	0.92[EUR][1000 genomes]
rs9988451	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
3	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
4	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
5	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
6	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
7	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45308800-45345400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:45309000-45315800	Weak transcription	Lung	lung
3	chr1:45309000-45324600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:45309000-45332600	Weak transcription	Spleen	Spleen
5	chr1:45309000-45335600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:45309200-45313400	Weak transcription	HepG2	liver
7	chr1:45309200-45313600	Weak transcription	Primary T cells from cord blood	blood
8	chr1:45309200-45313600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:45309200-45314000	Weak transcription	Right Ventricle	heart
10	chr1:45309200-45314200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:45309200-45314400	Weak transcription	Aorta	Aorta
12	chr1:45309200-45314800	Weak transcription	Left Ventricle	heart
13	chr1:45309200-45316000	Weak transcription	Pancreas	Pancrea
14	chr1:45309200-45316200	Weak transcription	Gastric	stomach
15	chr1:45309200-45323200	Weak transcription	HSMM	muscle
16	chr1:45309200-45336800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:45309200-45337800	Weak transcription	Psoas Muscle	Psoas
18	chr1:45309200-45343000	Weak transcription	Esophagus	oesophagus
19	chr1:45309200-45345200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:45309200-45360600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:45309400-45313400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:45309400-45313400	Weak transcription	Brain Germinal Matrix	brain
23	chr1:45309400-45313400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:45309400-45313600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:45309400-45313600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:45309400-45313800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:45309400-45313800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:45309400-45313800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:45309400-45313800	Weak transcription	Brain Substantia Nigra	brain
30	chr1:45309400-45314000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:45309400-45314000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:45309400-45314000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:45309400-45314200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:45309400-45314200	Weak transcription	Fetal Kidney	kidney
35	chr1:45309400-45314400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:45309400-45314600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:45309400-45314600	Weak transcription	Fetal Thymus	thymus
38	chr1:45309400-45314800	Weak transcription	NHEK	skin
39	chr1:45309400-45315000	Weak transcription	Placenta	Placenta
40	chr1:45309400-45315200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:45309400-45315400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:45309400-45315400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:45309400-45315400	Weak transcription	Osteobl	bone
44	chr1:45309400-45315600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:45309400-45315600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:45309400-45315600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:45309400-45315600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:45309400-45315600	Weak transcription	K562	blood
49	chr1:45309400-45315800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:45309400-45315800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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