Variant report

Variant	rs12539994
Chromosome Location	chr7:100659983-100659984
allele	G/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	STAT1	chr7:100659934-100660077	GM12878	blood:	n/a	n/a
2	MAZ	chr7:100659927-100660118	GM12878	blood:	n/a	n/a
3	ELF1	chr7:100659802-100661122	GM12878	blood:	n/a	chr7:100660411-100660422
4	EGR1	chr7:100659889-100660107	GM12878	blood:	n/a	chr7:100659971-100659985 chr7:100660020-100660034
5	POLR2A	chr7:100659947-100661073	GM19193	blood:	n/a	n/a
6	POLR2A	chr7:100659915-100661066	GM19099	blood:	n/a	n/a
7	SIN3A	chr7:100659980-100660985	H1-hESC	embryonic stem cell:	n/a	chr7:100660369-100660382
8	POLR2A	chr7:100659891-100661221	GM12892	blood:	n/a	n/a
9	POLR2A	chr7:100659968-100661057	H1-hESC	embryonic stem cell:	n/a	n/a
10	EGR1	chr7:100659817-100660181	K562	blood:	n/a	chr7:100659971-100659985 chr7:100660020-100660034
11	MAZ	chr7:100659685-100661326	IMR90	lung:	n/a	chr7:100660284-100660294
12	EGR1	chr7:100659814-100660156	K562	blood:	n/a	chr7:100659971-100659985 chr7:100660020-100660034
13	POLR2A	chr7:100659929-100661122	GM12878	blood:	n/a	n/a
14	RELA	chr7:100659944-100661132	GM12891	blood:	n/a	n/a
15	ZEB1	chr7:100659923-100660153	GM12878	blood:	n/a	n/a
16	RELA	chr7:100659882-100661143	GM18951	blood:	n/a	n/a
17	POLR2A	chr7:100659959-100660214	GM12878	blood:	n/a	n/a
18	ELF1	chr7:100659915-100661100	K562	blood:	n/a	chr7:100660411-100660422
19	CTBP2	chr7:100659966-100661045	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr7:100659944-100661288	GM12878	blood:	n/a	n/a
21	CHD1	chr7:100659894-100661148	IMR90	lung:	n/a	n/a
22	ZBTB7A	chr7:100659896-100661133	K562	blood:	n/a	n/a
23	POLR2A	chr7:100659841-100661067	IMR90	lung:	n/a	n/a
24	ELF1	chr7:100659807-100661135	K562	blood:	n/a	chr7:100660411-100660422
25	SPI1	chr7:100659806-100660067	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100486083..100488238-chr7:100659648..100662388,2	MCF-7	breast:
2	chr7:100462781..100465423-chr7:100657982..100660007,2	MCF-7	breast:
3	chr7:100606234..100609871-chr7:100659072..100662376,5	K562	blood:

Variant related genes	Relation type
MUC12	TF binding region
MUC17	TF binding region
ENSG00000176125	Chromatin interaction
ENSG00000087077	Chromatin interaction
ENSG00000225946	Chromatin interaction
ENSG00000169894	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs13231099	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13242391	0.84[EUR][1000 genomes]
rs6973913	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv1826021	chr7:100525848-100749246	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1846644	chr7:100525848-100749246	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1822460	chr7:100606044-100749246	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv427796	chr7:100606044-100749246	Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv428181	chr7:100606044-100749246	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription 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	26 gene(s)	inside rSNPs	diseases
9	nsv831074	chr7:100606051-100745532	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	esv1836983	chr7:100630638-100669857	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
13	esv1849981	chr7:100633668-100686761	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv1828583	chr7:100652181-100676353	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv1823966	chr7:100652181-100693849	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv3352938	chr7:100659732-100663130	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12539994	ENSG00000169887	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100635400-100660000	Weak transcription	Gastric	stomach
2	chr7:100635800-100660000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:100635800-100660200	Weak transcription	Right Atrium	heart
4	chr7:100647800-100660200	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr7:100651600-100660000	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:100652600-100660000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:100653800-100660000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:100653800-100660000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:100656600-100660000	Weak transcription	Thymus	Thymus
10	chr7:100657000-100660000	Weak transcription	HSMMtube	muscle
11	chr7:100657400-100660000	Weak transcription	Fetal Brain Male	brain
12	chr7:100657600-100660000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr7:100657600-100660000	Weak transcription	Fetal Intestine Small	intestine
14	chr7:100657600-100660000	Weak transcription	Ovary	ovary
15	chr7:100657600-100660000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:100659000-100660000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:100659000-100661000	Enhancers	Spleen	Spleen
18	chr7:100659200-100660000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:100659200-100660000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr7:100659200-100660000	Enhancers	Fetal Intestine Large	intestine
21	chr7:100659200-100660000	Enhancers	Stomach Mucosa	stomach
22	chr7:100659400-100660000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:100659400-100660000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:100659600-100660000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:100659600-100660000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:100659600-100660000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:100659600-100660000	Weak transcription	Colonic Mucosa	Colon
28	chr7:100659600-100660600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr7:100659600-100661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr7:100659600-100661200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:100659600-100661200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr7:100659600-100662000	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr7:100659800-100660000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr7:100659800-100660000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:100659800-100660000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:100659800-100660000	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr7:100659800-100660000	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr7:100659800-100660000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr7:100659800-100660000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr7:100659800-100660000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr7:100659800-100660000	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr7:100659800-100660000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr7:100659800-100660000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:100659800-100660000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:100659800-100660000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:100659800-100660000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:100659800-100660000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr7:100659800-100660000	Enhancers	A549	lung
49	chr7:100659800-100660000	Enhancers	HMEC	breast
50	chr7:100659800-100660000	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links