Variant report

Variant	rs12056593
Chromosome Location	chr8:11661467-11661468
allele	A/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	MAX	chr8:11659548-11661745	Hela-S3	cervix:	n/a	chr8:11659821-11659832 chr8:11661370-11661381 chr8:11659824-11659833 chr8:11659821-11659831
2	GATA1	chr8:11659383-11661536	K562	blood:	n/a	chr8:11660827-11660836 chr8:11661051-11661061 chr8:11661052-11661061
3	MTA3	chr8:11661159-11662106	GM12878	blood:	n/a	n/a
4	ZNF143	chr8:11661458-11661570	K562	blood:	n/a	n/a
5	POLR2A	chr8:11657712-11662103	GM12891	blood:	n/a	n/a
6	TBP	chr8:11660689-11661471	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr8:11659588-11662078	GM12878	blood:	n/a	chr8:11659821-11659830
8	MXI1	chr8:11660961-11661525	K562	blood:	n/a	n/a
9	BRCA1	chr8:11660658-11661794	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr8:11659169-11662162	MCF10A-Er-Src	breast:	n/a	n/a
11	IRF1	chr8:11659609-11662004	K562	blood:	n/a	chr8:11661419-11661431 chr8:11660186-11660200 chr8:11660115-11660124 chr8:11660081-11660090 chr8:11661361-11661373
12	MXI1	chr8:11659716-11661558	Hela-S3	cervix:	n/a	chr8:11659821-11659830
13	MXI1	chr8:11659343-11661982	SK-N-SH	brain:	n/a	chr8:11659821-11659830
14	MXI1	chr8:11659407-11661479	IMR90	lung:	n/a	chr8:11659821-11659830
15	POLR2A	chr8:11659369-11662049	K562	blood:	n/a	n/a
16	POLR2A	chr8:11659475-11672720	K562	blood:	n/a	n/a
17	MYC	chr8:11660768-11661794	MCF10A-Er-Src	breast:	n/a	chr8:11661370-11661381
18	GATA2	chr8:11660580-11661514	HUVEC	blood vessel:	n/a	chr8:11660826-11660840 chr8:11660827-11660836 chr8:11661051-11661061 chr8:11661052-11661061
19	GATA1	chr8:11659640-11661812	PBDE	blood:	n/a	chr8:11660827-11660836 chr8:11661051-11661061 chr8:11661052-11661061
20	JUN	chr8:11660654-11661493	K562	blood:	n/a	n/a
21	MYC	chr8:11659532-11661800	K562	blood:	n/a	chr8:11659821-11659832 chr8:11661370-11661381 chr8:11659824-11659833 chr8:11659821-11659831
22	MAX	chr8:11659541-11661518	A549	lung:	n/a	chr8:11659821-11659832 chr8:11661370-11661381 chr8:11659824-11659833 chr8:11659821-11659831
23	POLR2A	chr8:11659292-11662127	HL-60	blood:	n/a	n/a
24	RFX5	chr8:11659476-11662077	SK-N-SH	brain:	n/a	chr8:11660080-11660089 chr8:11660116-11660125
25	SIN3A	chr8:11659497-11661895	H1-hESC	embryonic stem cell:	n/a	chr8:11659737-11659750 chr8:11660895-11660908
26	POLR2A	chr8:11659209-11661487	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr8:11659397-11661798	MCF10A-Er-Src	breast:	n/a	n/a
28	REST	chr8:11659330-11662131	H1-neurons	neurons:	n/a	chr8:11659737-11659750 chr8:11660630-11660643 chr8:11659579-11659587 chr8:11660895-11660908

No.	Distal block	Cell Line	Cell type
1	chr8:11645433..11648215-chr8:11658187..11661640,5	MCF-7	breast:
2	chr8:11660132..11662159-chr8:11687088..11688698,2	MCF-7	breast:
3	chr8:11658864..11661745-chr8:11724576..11726431,3	MCF-7	breast:
4	chr8:11658229..11662389-chr8:11662980..11669380,10	MCF-7	breast:
5	chr8:11659426..11661474-chr8:11724613..11726870,3	MCF-7	breast:
6	chr8:11658127..11661675-chr8:11664375..11667732,3	K562	blood:
7	chr8:11626596..11628658-chr8:11659514..11662088,3	K562	blood:
8	chr8:11624784..11628111-chr8:11660073..11663416,4	MCF-7	breast:

Variant related genes	Relation type
FDFT1	TF binding region
ENSG00000255046	TF binding region
ENSG00000227203	Chromatin interaction
ENSG00000154328	Chromatin interaction
ENSG00000164733	Chromatin interaction
ENSG00000079459	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11985225	1.00[CEU][hapmap]
rs12542790	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12542839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12543505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12545407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17524874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17524888	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17553545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17553559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2686189	0.87[ASN][1000 genomes]
rs6730	1.00[CEU][hapmap]
rs6991234	1.00[CHB][hapmap]
rs7009514	1.00[CHB][hapmap]
rs7013950	1.00[CHB][hapmap]
rs73207248	0.87[ASN][1000 genomes]
rs7824015	0.86[ASN][1000 genomes]
rs7824481	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription 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	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1032739	chr8:11643803-11716473	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv890363	chr8:11647941-11681825	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv890364	chr8:11654796-11671041	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1034132	chr8:11657033-12198242	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 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	chr8:11658400-11666800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:11659000-11663400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr8:11659200-11663200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr8:11659400-11661600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:11659400-11661600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr8:11659400-11661800	Active TSS	A549	lung
7	chr8:11659400-11662600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr8:11659400-11663800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr8:11659600-11661600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:11659600-11661600	Active TSS	Brain Angular Gyrus	brain
11	chr8:11659600-11661600	Active TSS	Right Atrium	heart
12	chr8:11659600-11661600	Active TSS	Hela-S3	cervix
13	chr8:11659600-11662000	Active TSS	Ovary	ovary
14	chr8:11659600-11662000	Active TSS	HSMM	muscle
15	chr8:11659600-11662200	Active TSS	Brain Cingulate Gyrus	brain
16	chr8:11659600-11662200	Active TSS	Esophagus	oesophagus
17	chr8:11659600-11662400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr8:11659600-11662400	Active TSS	Small Intestine	intestine
19	chr8:11659600-11662600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr8:11659600-11662600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:11659600-11663000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr8:11659600-11663200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr8:11659600-11663200	Active TSS	Fetal Brain Female	brain
24	chr8:11659600-11663400	Active TSS	Fetal Brain Male	brain
25	chr8:11659600-11663400	Active TSS	NHLF	lung
26	chr8:11659600-11663600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr8:11659600-11664200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr8:11659600-11664200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr8:11659800-11661600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:11659800-11661600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr8:11659800-11661600	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr8:11659800-11661600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr8:11659800-11661600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr8:11659800-11661600	Active TSS	NHDF-Ad	bronchial
35	chr8:11659800-11661800	Active TSS	Lung	lung
36	chr8:11659800-11661800	Active TSS	HMEC	breast
37	chr8:11659800-11661800	Active TSS	NHEK	skin
38	chr8:11659800-11662000	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr8:11659800-11662000	Active TSS	Fetal Stomach	stomach
40	chr8:11659800-11662000	Active TSS	Thymus	Thymus
41	chr8:11659800-11662400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr8:11659800-11662600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr8:11659800-11662600	Active TSS	HSMMtube	muscle
44	chr8:11659800-11662600	Active TSS	K562	blood
45	chr8:11659800-11662800	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr8:11659800-11663600	Active TSS	GM12878-XiMat	blood
47	chr8:11659800-11664200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr8:11660000-11661600	Active TSS	NH-A	brain
49	chr8:11660000-11662000	Active TSS	Colonic Mucosa	Colon
50	chr8:11660000-11662400	Active TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links