Variant report

Variant	rs7594727
Chromosome Location	chr2:97489870-97489871
allele	A/C
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	FOXA1	chr2:97489750-97490185	HepG2	liver:	n/a	chr2:97489981-97489993
2	NFIC	chr2:97489743-97490198	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr2:97489683-97490232	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr2:97489775-97489900	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXA1	chr2:97489781-97490179	HepG2	liver:	n/a	chr2:97489981-97489993
6	FOXA1	chr2:97489775-97490204	HepG2	liver:	n/a	chr2:97489981-97489993
7	TEAD4	chr2:97489787-97490179	MCF-7	breast:	n/a	n/a
8	FOXA1	chr2:97489780-97490191	ECC-1	luminal epithelium:	n/a	chr2:97489981-97489993
9	FOXA1	chr2:97489843-97490206	HepG2	liver:	n/a	chr2:97489981-97489993
10	TEAD4	chr2:97489734-97490222	ECC-1	luminal epithelium:	n/a	n/a
11	FOXA1	chr2:97489835-97490119	T-47D	breast:	n/a	chr2:97489981-97489993
12	TEAD4	chr2:97489688-97490305	HepG2	liver:	n/a	n/a
13	FOXA1	chr2:97489749-97490152	T-47D	breast:	n/a	chr2:97489981-97489993
14	FOXA2	chr2:97489806-97490152	HepG2	liver:	n/a	chr2:97489981-97489993
15	FOXA2	chr2:97489830-97490284	A549	lung:	n/a	chr2:97489981-97489993
16	SRF	chr2:97489813-97490366	MCF-7	breast:	n/a	n/a
17	SRF	chr2:97489837-97490229	ECC-1	luminal epithelium:	n/a	n/a
18	SRF	chr2:97489726-97490170	MCF-7	breast:	n/a	n/a
19	MAFK	chr2:97489520-97490028	IMR90	lung:	n/a	n/a
20	POLR2A	chr2:97489732-97490198	PANC-1	pancreas:	n/a	n/a
21	FOXA2	chr2:97489765-97490210	A549	lung:	n/a	chr2:97489981-97489993
22	FOXA1	chr2:97489809-97490064	ECC-1	luminal epithelium:	n/a	chr2:97489981-97489993

No.	Distal block	Cell Line	Cell type
1	chr2:97426560..97429669-chr2:97487357..97491316,3	MCF-7	breast:
2	chr2:97485243..97487590-chr2:97488135..97490433,3	K562	blood:
3	chr2:97488123..97491381-chr2:97522097..97525123,6	MCF-7	breast:
4	chr2:97488060..97490357-chr2:97534412..97536411,3	MCF-7	breast:
5	chr2:97489114..97491853-chr2:97492088..97494709,3	K562	blood:

Variant related genes	Relation type
CNNM3	TF binding region
ENSG00000213337	Chromatin interaction
ENSG00000158158	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000168763	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11897786	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12846	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320146	0.87[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs1320149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419073	0.87[CEU][hapmap];0.85[AMR][1000 genomes]
rs17119598	0.87[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2276654	0.87[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs3731941	0.88[MEX][hapmap];0.82[TSI][hapmap]
rs55674661	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58147284	0.85[AMR][1000 genomes]
rs62152793	0.82[EUR][1000 genomes]
rs62152794	0.80[EUR][1000 genomes]
rs62152795	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576986	0.87[CEU][hapmap]
rs6576987	0.87[CEU][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs6576989	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6753987	1.00[MEX][hapmap];0.88[TSI][hapmap]
rs7580942	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7608621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9948	0.87[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs9973492	0.87[CEU][hapmap]

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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7594727	FAHD2CP	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97483000-97490800	Enhancers	Fetal Heart	heart
2	chr2:97483600-97490000	Weak transcription	NH-A	brain
3	chr2:97483600-97492200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:97483600-97493400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:97483600-97493400	Weak transcription	HSMMtube	muscle
6	chr2:97483600-97498200	Weak transcription	HSMM	muscle
7	chr2:97483800-97490000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr2:97483800-97492200	Weak transcription	NHLF	lung
9	chr2:97483800-97493200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:97483800-97493400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:97483800-97493600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:97483800-97494400	Weak transcription	Osteobl	bone
13	chr2:97483800-97498400	Weak transcription	NHDF-Ad	bronchial
14	chr2:97484000-97493200	Weak transcription	Fetal Kidney	kidney
15	chr2:97484000-97493600	Weak transcription	NHEK	skin
16	chr2:97484600-97518400	Weak transcription	HUVEC	blood vessel
17	chr2:97484800-97493600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:97485200-97490800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:97485200-97490800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:97485200-97498400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:97485600-97493400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:97485800-97490600	Genic enhancers	Fetal Intestine Small	intestine
23	chr2:97486000-97505000	Strong transcription	Fetal Stomach	stomach
24	chr2:97486600-97490800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:97486600-97491600	Weak transcription	Primary B cells from cord blood	blood
26	chr2:97486600-97492200	Weak transcription	K562	blood
27	chr2:97486600-97492600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:97486600-97498000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:97486800-97490800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:97486800-97500800	Strong transcription	Thymus	Thymus
31	chr2:97487000-97498800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr2:97487200-97490400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:97487200-97490600	Genic enhancers	HepG2	liver
34	chr2:97487200-97490800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:97487200-97491200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:97487200-97501800	Strong transcription	Primary T cells from cord blood	blood
37	chr2:97487200-97504000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:97487400-97490600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:97487400-97499200	Weak transcription	Fetal Brain Male	brain
40	chr2:97487400-97501800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:97487400-97504200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:97487600-97490000	Weak transcription	Fetal Lung	lung
43	chr2:97487600-97491000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:97487600-97491800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:97487600-97492000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr2:97487600-97492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:97487600-97493400	Weak transcription	Small Intestine	intestine
48	chr2:97487600-97493800	Weak transcription	GM12878-XiMat	blood
49	chr2:97487600-97504600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:97488000-97497400	Strong transcription	Spleen	Spleen

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