Variant report

Variant	rs852539
Chromosome Location	chr7:5592706-5592707
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	chr7:5592457-5592822	Hela-S3	cervix:	n/a	n/a
2	HNF4A	chr7:5592327-5592787	HepG2	liver:	n/a	chr7:5592604-5592612 chr7:5592601-5592614 chr7:5592600-5592614 chr7:5592600-5592614 chr7:5592600-5592613 chr7:5592598-5592616 chr7:5592599-5592614 chr7:5592601-5592613 chr7:5592601-5592613 chr7:5592601-5592613 chr7:5592596-5592618 chr7:5592600-5592614 chr7:5592605-5592623
3	SP1	chr7:5592338-5592791	HepG2	liver:	n/a	chr7:5592538-5592552
4	NR3C1	chr7:5592317-5592756	A549	lung:	n/a	chr7:5592517-5592531
5	MAX	chr7:5592475-5592726	K562	blood:	n/a	n/a
6	HNF4A	chr7:5592364-5592756	HepG2	liver:	n/a	chr7:5592604-5592612 chr7:5592601-5592614 chr7:5592600-5592614 chr7:5592600-5592614 chr7:5592600-5592613 chr7:5592598-5592616 chr7:5592599-5592614 chr7:5592601-5592613 chr7:5592601-5592613 chr7:5592601-5592613 chr7:5592596-5592618 chr7:5592600-5592614 chr7:5592605-5592623
7	HDAC2	chr7:5592378-5592738	HepG2	liver:	n/a	n/a
8	RFX5	chr7:5592460-5592720	Hela-S3	cervix:	n/a	n/a
9	NR2F2	chr7:5592434-5592802	K562	blood:	n/a	n/a
10	NR2F2	chr7:5592312-5593354	K562	blood:	n/a	n/a
11	NFIC	chr7:5592441-5592744	HepG2	liver:	n/a	n/a
12	BHLHE40	chr7:5592423-5592716	HepG2	liver:	n/a	n/a
13	POLR2A	chr7:5592434-5592789	Hela-S3	cervix:	n/a	n/a
14	HCFC1	chr7:5592241-5592777	Hela-S3	cervix:	n/a	n/a
15	MYBL2	chr7:5592355-5592798	HepG2	liver:	n/a	n/a
16	HNF4A	chr7:5592395-5592824	HepG2	liver:	n/a	chr7:5592604-5592612 chr7:5592601-5592614 chr7:5592600-5592614 chr7:5592600-5592614 chr7:5592600-5592613 chr7:5592598-5592616 chr7:5592599-5592614 chr7:5592601-5592613 chr7:5592601-5592613 chr7:5592601-5592613 chr7:5592596-5592618 chr7:5592600-5592614 chr7:5592605-5592623
17	POLR2A	chr7:5592380-5593459	Hela-S3	cervix:	n/a	n/a
18	HNF4G	chr7:5592324-5592777	HepG2	liver:	n/a	chr7:5592604-5592612 chr7:5592601-5592614 chr7:5592600-5592614 chr7:5592600-5592614 chr7:5592600-5592613 chr7:5592598-5592616 chr7:5592601-5592613 chr7:5592601-5592613 chr7:5592601-5592613 chr7:5592596-5592618 chr7:5592600-5592614 chr7:5592605-5592623

No.	Distal block	Cell Line	Cell type
1	chr7:5558806..5574463-chr7:5583405..5604290,160	MCF-7	breast:
2	chr7:5543445..5545734-chr7:5591594..5593277,2	K562	blood:
3	chr7:5320876..5323087-chr7:5592627..5594710,2	K562	blood:
4	chr7:5563943..5564839-chr7:5592706..5593258,2	MCF-7	breast:
5	chr7:5464020..5466860-chr7:5591576..5593139,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272719	TF binding region
ENSG00000263900	Chromatin interaction
ENSG00000272953	Chromatin interaction
ENSG00000182095	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000164638	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2908421	0.85[ASN][1000 genomes]
rs852492	0.83[ASN][1000 genomes]
rs852496	0.80[ASN][1000 genomes]
rs852501	0.85[ASN][1000 genomes]
rs852503	0.85[ASN][1000 genomes]
rs852504	0.85[ASN][1000 genomes]
rs852509	0.85[ASN][1000 genomes]
rs852513	0.81[ASN][1000 genomes]
rs852528	0.85[ASN][1000 genomes]
rs852534	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852535	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852537	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852538	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852540	1.00[ASN][1000 genomes]
rs852541	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	333 gene(s)	inside rSNPs	diseases
5	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
6	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
7	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
8	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
9	nsv887407	chr7:5432672-5605130	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	302 gene(s)	inside rSNPs	diseases
10	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
11	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
13	nsv887413	chr7:5521468-5607884	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	279 gene(s)	inside rSNPs	diseases
14	nsv1025434	chr7:5537571-5705283	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription 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	297 gene(s)	inside rSNPs	diseases
15	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
16	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
17	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
18	nsv887414	chr7:5584934-5667645	Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
19	nsv887415	chr7:5584934-5675305	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
20	nsv887416	chr7:5584934-5695259	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5572600-5594600	Weak transcription	Right Atrium	heart
2	chr7:5587000-5594200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr7:5588800-5595000	Enhancers	Placenta	Placenta
4	chr7:5589000-5594400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:5589400-5593000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:5589400-5593000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr7:5589400-5594000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:5589400-5594200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:5589400-5594200	Weak transcription	Primary B cells from cord blood	blood
10	chr7:5589400-5594200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr7:5589400-5594200	Weak transcription	Spleen	Spleen
12	chr7:5589400-5594400	Weak transcription	HUVEC	blood vessel
13	chr7:5589400-5595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:5589400-5595200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:5589600-5592800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:5589600-5592800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:5589600-5593000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:5589600-5593000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr7:5589600-5593000	Weak transcription	HMEC	breast
20	chr7:5589600-5593000	Weak transcription	HSMM	muscle
21	chr7:5589600-5594000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:5589600-5594200	Weak transcription	Esophagus	oesophagus
23	chr7:5589600-5594200	Weak transcription	Lung	lung
24	chr7:5589600-5594400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:5589600-5594400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:5589600-5594400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:5589600-5594400	Weak transcription	NHDF-Ad	bronchial
28	chr7:5589600-5594600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr7:5589600-5594800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:5589600-5595000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:5589600-5595000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:5589600-5595200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:5589800-5594400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:5590000-5594000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr7:5590000-5594200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:5590200-5592800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr7:5590200-5594200	Weak transcription	NH-A	brain
38	chr7:5590400-5593000	Weak transcription	NHEK	skin
39	chr7:5590400-5594200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:5590600-5594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:5590600-5594400	Weak transcription	Gastric	stomach
42	chr7:5590800-5594000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:5590800-5594200	Weak transcription	Ovary	ovary
44	chr7:5591600-5593000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr7:5591600-5593000	Enhancers	Fetal Intestine Small	intestine
46	chr7:5591600-5595000	Enhancers	Fetal Intestine Large	intestine
47	chr7:5591800-5593400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:5591800-5594400	Enhancers	Colonic Mucosa	Colon
49	chr7:5591800-5595000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:5592000-5594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links