Variant report

Variant	rs12102130
Chromosome Location	chr15:78327757-78327758
allele	A/G
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	chr15:78327592-78328014	HL-60	blood:	n/a	n/a
2	MAX	chr15:78326243-78328842	NB4	blood:	n/a	chr15:78326421-78326432 chr15:78326515-78326524
3	POLR2A	chr15:78326599-78328151	HL-60	blood:	n/a	n/a
4	RELA	chr15:78326745-78327888	GM18951	blood:	n/a	n/a
5	EP300	chr15:78327506-78327795	GM12878	blood:	n/a	n/a
6	RUNX3	chr15:78326677-78327945	GM12878	blood:	n/a	chr15:78327781-78327790 chr15:78327781-78327790
7	MTA3	chr15:78326588-78327904	GM12878	blood:	n/a	n/a
8	MYC	chr15:78326363-78328390	NB4	blood:	n/a	chr15:78326421-78326432 chr15:78326515-78326524
9	RUNX3	chr15:78326657-78328036	GM12878	blood:	n/a	chr15:78327781-78327790 chr15:78327781-78327790
10	CTCF	chr15:78327740-78327890	HCPEpiC	choroid plexus:	n/a	n/a
11	FOS	chr15:78327545-78328428	HUVEC	blood vessel:	n/a	chr15:78327994-78328005
12	MAFK	chr15:78327196-78328340	IMR90	lung:	n/a	chr15:78327939-78327954 chr15:78327989-78328004

No.	Distal block	Cell Line	Cell type
1	chr15:78326298..78328930-chr15:78337722..78339392,2	MCF-7	breast:
2	chr15:78326751..78329240-chr15:78339256..78341988,2	K562	blood:
3	chr15:78326771..78328887-chr15:78329964..78334195,3	K562	blood:

Variant related genes	Relation type
MIR1827	TF binding region
ENSG00000221476	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10519182	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11629761	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs11639164	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11854491	0.87[AMR][1000 genomes]
rs13329101	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13329302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969367	1.00[YRI][hapmap]
rs16969405	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969407	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969408	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969414	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969423	1.00[YRI][hapmap]
rs16969424	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969430	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969447	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs1985487	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28394000	0.91[AFR][1000 genomes]
rs28417785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28441175	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28451835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470811	0.87[AMR][1000 genomes]
rs28485414	0.83[AFR][1000 genomes]
rs28491609	0.88[AFR][1000 genomes]
rs28491820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28519575	0.91[AFR][1000 genomes]
rs28526757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28579273	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28581571	0.93[AFR][1000 genomes]
rs28590577	0.86[AFR][1000 genomes]
rs28591625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28647720	0.93[AFR][1000 genomes]
rs28674965	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55930913	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58247186	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7167778	0.87[AMR][1000 genomes]
rs74027705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74027706	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74027709	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74029754	0.87[AMR][1000 genomes]
rs7495639	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920647	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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 target site	80 gene(s)	inside rSNPs	diseases
2	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78301400-78342200	Weak transcription	HMEC	breast
3	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:78305400-78329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:78309200-78330200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:78309200-78330800	Weak transcription	A549	lung
8	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:78316000-78332400	Weak transcription	Hela-S3	cervix
10	chr15:78317000-78327800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:78317400-78342600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:78317800-78331000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:78320200-78334400	Weak transcription	Aorta	Aorta
17	chr15:78320400-78331800	Weak transcription	Esophagus	oesophagus
18	chr15:78321200-78343800	Weak transcription	NHEK	skin
19	chr15:78322200-78336600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:78322200-78341000	Weak transcription	Brain Germinal Matrix	brain
21	chr15:78322400-78336600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:78324000-78332200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr15:78324400-78330400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:78324600-78328400	Enhancers	Primary B cells from peripheral blood	blood
25	chr15:78324600-78334400	Weak transcription	Ovary	ovary
26	chr15:78325600-78337800	Genic enhancers	Fetal Thymus	thymus
27	chr15:78325800-78333600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr15:78326000-78331600	Enhancers	HUVEC	blood vessel
29	chr15:78326200-78327800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr15:78326200-78328000	Flanking Active TSS	GM12878-XiMat	blood
31	chr15:78326200-78328400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr15:78326200-78328600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:78326200-78328600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:78326200-78328600	Enhancers	Brain Hippocampus Middle	brain
35	chr15:78326200-78328600	Enhancers	Fetal Kidney	kidney
36	chr15:78326200-78328600	Enhancers	NHDF-Ad	bronchial
37	chr15:78326200-78329000	Enhancers	Brain Substantia Nigra	brain
38	chr15:78326200-78332000	Genic enhancers	Fetal Intestine Small	intestine
39	chr15:78326200-78332800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:78326400-78328400	Genic enhancers	Fetal Stomach	stomach
41	chr15:78326400-78328600	Enhancers	Brain Angular Gyrus	brain
42	chr15:78326400-78328800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr15:78326400-78331600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr15:78326400-78332000	Genic enhancers	Fetal Muscle Leg	muscle
45	chr15:78326600-78328000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:78326600-78328000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr15:78326600-78328000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:78326600-78328200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr15:78326600-78328400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:78326600-78328400	Genic enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links