Variant report

Variant	rs3756819
Chromosome Location	chr6:24665340-24665341
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	POLR2A	chr6:24662292-24665727	K562	blood:	n/a	n/a
2	FOXA1	chr6:24665297-24665852	HepG2	liver:	n/a	n/a
3	HCFC1	chr6:24665333-24668321	Hela-S3	cervix:	n/a	n/a
4	FOXA1	chr6:24665275-24665803	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:24665066-24665695	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
2	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:
3	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:

Variant related genes	Relation type
ACOT13	TF binding region
ENSG00000112308	Chromatin interaction
ENSG00000137261	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1061925	0.88[GIH][hapmap]
rs11961837	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11962639	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17243157	0.88[GIH][hapmap]
rs2143340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181234	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777665	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6909884	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73392549	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7768291	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3756819	ZNF192	cis	parietal	SCAN
rs3756819	ACOT13	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24646800-24666000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:24647000-24666400	Weak transcription	Esophagus	oesophagus
3	chr6:24653800-24666200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:24656200-24666000	Weak transcription	Aorta	Aorta
5	chr6:24657400-24665400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:24658400-24665600	Strong transcription	HSMM	muscle
7	chr6:24660000-24665400	Weak transcription	NHDF-Ad	bronchial
8	chr6:24660200-24665600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:24660600-24666200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:24661600-24665600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr6:24662200-24665400	Strong transcription	Fetal Muscle Leg	muscle
12	chr6:24662600-24665400	Weak transcription	Right Atrium	heart
13	chr6:24662600-24666400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:24662800-24665400	Strong transcription	Osteobl	bone
15	chr6:24662800-24665800	Transcr. at gene 5' and 3'	A549	lung
16	chr6:24663000-24666200	Weak transcription	Pancreas	Pancrea
17	chr6:24663600-24665600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr6:24663600-24666200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:24663800-24665400	Enhancers	Liver	Liver
20	chr6:24663800-24665400	Active TSS	Rectal Smooth Muscle	rectum
21	chr6:24663800-24665400	Weak transcription	HUVEC	blood vessel
22	chr6:24663800-24665800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:24663800-24666200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:24664000-24666000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:24664000-24666000	Weak transcription	Right Ventricle	heart
26	chr6:24664000-24666200	Weak transcription	Gastric	stomach
27	chr6:24664000-24666200	Weak transcription	Left Ventricle	heart
28	chr6:24664000-24666200	Weak transcription	Lung	lung
29	chr6:24664000-24666400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:24664000-24668600	Active TSS	Colonic Mucosa	Colon
31	chr6:24664200-24666000	Genic enhancers	Primary T cells from cord blood	blood
32	chr6:24664400-24665400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr6:24664400-24665400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:24664400-24665400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:24664400-24665400	Weak transcription	Psoas Muscle	Psoas
36	chr6:24664400-24665400	Weak transcription	NHLF	lung
37	chr6:24664400-24665600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:24664400-24665600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr6:24664400-24665800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr6:24664400-24668000	Active TSS	Fetal Intestine Large	intestine
41	chr6:24664600-24665400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:24664600-24665400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:24664600-24665400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:24664600-24665400	Genic enhancers	Fetal Brain Male	brain
45	chr6:24664600-24665400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:24664600-24665600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
47	chr6:24664600-24665800	Flanking Active TSS	Fetal Brain Female	brain
48	chr6:24664600-24666000	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr6:24664600-24668000	Active TSS	Fetal Intestine Small	intestine
50	chr6:24664800-24665400	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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