Variant report

Variant	rs2412692
Chromosome Location	chr4:56718312-56718313
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	MXI1	chr4:56718157-56718363	HepG2	liver:	n/a	n/a
2	TEAD4	chr4:56717937-56718504	HepG2	liver:	n/a	n/a
3	HNF4A	chr4:56718028-56718434	HepG2	liver:	n/a	chr4:56718221-56718236
4	STAT3	chr4:56718185-56718419	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr4:56718005-56718434	HepG2	liver:	n/a	n/a
6	FOS	chr4:56718129-56718443	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr4:56717968-56718464	HepG2	liver:	n/a	n/a
8	STAT3	chr4:56718216-56718385	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF7L2	chr4:56718172-56718511	MCF-7	breast:	n/a	n/a
10	MYC	chr4:56718123-56718528	MCF10A-Er-Src	breast:	n/a	n/a
11	HEY1	chr4:56718013-56718432	HepG2	liver:	n/a	n/a
12	MYC	chr4:56718017-56718456	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr4:56718191-56718417	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr4:56718122-56718513	MCF10A-Er-Src	breast:	n/a	n/a
15	ELF1	chr4:56718119-56718435	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:56718107-56718356	MCF10A-Er-Src	breast:	n/a	n/a
17	HNF4A	chr4:56718033-56718424	HepG2	liver:	n/a	chr4:56718221-56718236
18	HNF4G	chr4:56718018-56718446	HepG2	liver:	n/a	chr4:56718222-56718237
19	BHLHE40	chr4:56718052-56718462	HepG2	liver:	n/a	n/a
20	FOS	chr4:56718107-56718527	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr4:56718151-56718316	MCF10A-Er-Src	breast:	n/a	n/a
22	GABPA	chr4:56718149-56718343	HepG2	liver:	n/a	n/a
23	ELF1	chr4:56718018-56718469	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56717893..56722441-chr4:56723240..56726712,5	MCF-7	breast:
2	chr4:56717920..56722163-chr4:56723001..56728347,7	K562	blood:
3	chr4:56712983..56715874-chr4:56716804..56719417,2	K562	blood:

Variant related genes	Relation type
EXOC1	TF binding region
ENSG00000090989	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10014018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13143281	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17797565	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1947128	0.88[YRI][hapmap]
rs1992813	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4352536	0.88[ASN][1000 genomes]
rs6554325	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824915	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2412692	LRRC66	cis	parietal	SCAN
rs2412692	C1orf201	trans	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56716000-56719200	Weak transcription	Right Atrium	heart
2	chr4:56716400-56719200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:56716400-56719200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:56716400-56719800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:56716600-56718600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:56716800-56719200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:56716800-56719800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:56716800-56719800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:56717400-56718400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:56717400-56719200	Enhancers	Duodenum Mucosa	Duodenum
11	chr4:56717400-56719400	Enhancers	HMEC	breast
12	chr4:56717600-56718400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:56717600-56718400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:56717600-56718400	Enhancers	Fetal Intestine Large	intestine
15	chr4:56717600-56718600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr4:56717600-56718600	Enhancers	Fetal Intestine Small	intestine
17	chr4:56717600-56718600	Flanking Active TSS	HepG2	liver
18	chr4:56717600-56719000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr4:56717600-56719200	Enhancers	Primary T cells from cord blood	blood
20	chr4:56717600-56719200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr4:56717600-56719200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr4:56717600-56719400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:56717600-56719400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:56717600-56719800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:56717800-56719200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:56717800-56719200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr4:56717800-56719400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr4:56718000-56718400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr4:56718000-56718400	Enhancers	Aorta	Aorta
30	chr4:56718000-56718400	Enhancers	Placenta	Placenta
31	chr4:56718000-56718400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr4:56718000-56718600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:56718000-56718600	Flanking Active TSS	NHEK	skin
34	chr4:56718000-56719200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:56718000-56719600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr4:56718200-56718400	Enhancers	Right Ventricle	heart
37	chr4:56718200-56718400	Bivalent Enhancer	Thymus	Thymus
38	chr4:56718200-56719200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr4:56718200-56719600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links