Variant report

Variant	rs17545656
Chromosome Location	chr7:7681695-7681696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr7:7681680-7681865	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr7:7678754-7682381	SK-N-SH	brain:	n/a	n/a
3	CBX3	chr7:7681630-7682044	K562	blood:	n/a	n/a
4	GATA3	chr7:7681687-7682855	MCF-7	breast:	n/a	n/a
5	POLR2A	chr7:7681692-7681882	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr7:7679088-7681837	PBDE	blood:	n/a	n/a
7	MYC	chr7:7681681-7682095	K562	blood:	n/a	n/a
8	FOXA1	chr7:7681671-7682066	HepG2	liver:	n/a	n/a
9	POLR2A	chr7:7681686-7681865	MCF10A-Er-Src	breast:	n/a	n/a
10	MAX	chr7:7681128-7682174	Hela-S3	cervix:	n/a	n/a
11	ZNF384	chr7:7681556-7682177	K562	blood:	n/a	n/a
12	RFX5	chr7:7677457-7682740	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:7603046..7608569-chr7:7677123..7682101,8	MCF-7	breast:
2	chr7:7680700..7683473-chr7:7685626..7688056,2	MCF-7	breast:
3	chr7:7673907..7678610-chr7:7678691..7681851,6	MCF-7	breast:
4	chr7:7623467..7625147-chr7:7680756..7682414,2	K562	blood:
5	chr7:7605830..7608267-chr7:7679102..7681869,5	MCF-7	breast:
6	chr7:7680697..7682834-chr7:8264362..8267648,3	K562	blood:

No data

Variant related genes	Relation type
RPA3	TF binding region
ENSG00000106399	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000164654	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12668835	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12669683	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1859605	0.92[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28912696	1.00[YRI][hapmap]
rs3823841	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4720748	0.85[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4720749	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67320211	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6974232	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs886724	0.92[CHB][hapmap]
rs9791866	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv1034199	chr7:7617835-7691176	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv606044	chr7:7652372-7727101	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv887479	chr7:7681131-7779091	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv887481	chr7:7681576-7779324	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7679000-7681800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:7679000-7682000	Active TSS	Fetal Intestine Small	intestine
3	chr7:7679200-7682000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:7679400-7682000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr7:7679600-7681800	Active TSS	Fetal Thymus	thymus
6	chr7:7679600-7682200	Active TSS	Colonic Mucosa	Colon
7	chr7:7680400-7681800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr7:7680600-7682000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:7680800-7681800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:7680800-7681800	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr7:7680800-7681800	Flanking Active TSS	Dnd41	blood
12	chr7:7681000-7681800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:7681000-7681800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr7:7681000-7681800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:7681000-7681800	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr7:7681000-7681800	Flanking Active TSS	Fetal Intestine Large	intestine
17	chr7:7681000-7681800	Flanking Active TSS	Fetal Kidney	kidney
18	chr7:7681000-7682000	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr7:7681000-7682000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr7:7681000-7682000	Enhancers	Spleen	Spleen
21	chr7:7681000-7682200	Flanking Active TSS	Hela-S3	cervix
22	chr7:7681200-7681800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:7681200-7681800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr7:7681200-7681800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr7:7681200-7681800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr7:7681200-7681800	Flanking Active TSS	Fetal Brain Female	brain
27	chr7:7681200-7681800	Flanking Active TSS	A549	lung
28	chr7:7681200-7681800	Flanking Active TSS	GM12878-XiMat	blood
29	chr7:7681200-7682000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr7:7681200-7682000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:7681200-7682000	Flanking Active TSS	HMEC	breast
32	chr7:7681200-7682600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr7:7681400-7681800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:7681400-7681800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr7:7681400-7681800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr7:7681400-7681800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr7:7681400-7681800	Enhancers	Adipose Nuclei	Adipose
38	chr7:7681400-7681800	Enhancers	Brain Hippocampus Middle	brain
39	chr7:7681400-7681800	Weak transcription	Esophagus	oesophagus
40	chr7:7681400-7681800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr7:7681400-7681800	Enhancers	HSMM	muscle
42	chr7:7681400-7682000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr7:7681400-7682000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr7:7681400-7682000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr7:7681400-7682000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr7:7681400-7682000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr7:7681400-7682000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:7681400-7682000	Enhancers	Brain Angular Gyrus	brain
49	chr7:7681400-7682000	Enhancers	Brain Anterior Caudate	brain
50	chr7:7681400-7682000	Enhancers	Fetal Brain Male	brain

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