Variant report

Variant	rs6797111
Chromosome Location	chr3:139257194-139257195
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	MXI1	chr3:139254870-139260531	SK-N-SH	brain:	n/a	n/a
2	FOSL1	chr3:139255939-139257885	HCT-116	colon:	n/a	chr3:139256357-139256365 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
3	JUND	chr3:139255655-139257823	SK-N-SH	brain:	n/a	chr3:139256357-139256365 chr3:139256355-139256366 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
4	BATF	chr3:139256984-139257258	GM12878	blood:	n/a	n/a
5	EP300	chr3:139251629-139259175	SK-N-SH	brain:	n/a	chr3:139256357-139256366 chr3:139253631-139253641 chr3:139252024-139252040 chr3:139256356-139256365
6	POLR2A	chr3:139256766-139257480	HCT-116	colon:	n/a	n/a
7	SIN3AK20	chr3:139256022-139258994	HCT-116	colon:	n/a	n/a
8	NFIC	chr3:139256919-139257321	GM12878	blood:	n/a	chr3:139257023-139257051 chr3:139257025-139257041
9	FOSL1	chr3:139255958-139257434	HCT-116	colon:	n/a	chr3:139256357-139256365 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
10	TCF7L2	chr3:139256709-139257982	HCT-116	colon:	n/a	chr3:139257148-139257157 chr3:139257147-139257156 chr3:139256975-139256989 chr3:139257144-139257160 chr3:139256977-139256986 chr3:139257149-139257156 chr3:139257144-139257160
11	JUND	chr3:139256007-139258019	HCT-116	colon:	n/a	chr3:139256357-139256365 chr3:139256355-139256366 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
12	CBX3	chr3:139256018-139258020	HCT-116	colon:	n/a	n/a
13	JUND	chr3:139255896-139258067	HCT-116	colon:	n/a	chr3:139256357-139256365 chr3:139256355-139256366 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
14	NFIC	chr3:139256768-139257299	ECC-1	luminal epithelium:	n/a	chr3:139257023-139257051 chr3:139257025-139257041
15	RUNX3	chr3:139256895-139257269	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:139256775-139258093	HCT-116	colon:	n/a	n/a
17	ELF1	chr3:139256766-139257239	GM12878	blood:	n/a	n/a
18	SP1	chr3:139255938-139258057	HCT-116	colon:	n/a	chr3:139256874-139256887
19	TCF7L2	chr3:139256262-139257423	Hela-S3	cervix:	n/a	chr3:139257148-139257157 chr3:139256356-139256365 chr3:139257147-139257156 chr3:139256975-139256989 chr3:139257144-139257160 chr3:139256977-139256986 chr3:139257149-139257156 chr3:139257144-139257160 chr3:139256357-139256366
20	SP1	chr3:139255901-139258032	HCT-116	colon:	n/a	chr3:139256874-139256887

Variant related genes	Relation type
ENSG00000248932	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10935331	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167188	0.89[EUR][1000 genomes]
rs176990	0.96[EUR][1000 genomes]
rs190910	0.96[EUR][1000 genomes]
rs211586	0.96[EUR][1000 genomes]
rs295497	0.90[ASN][1000 genomes]
rs295498	0.93[ASN][1000 genomes]
rs295501	0.86[EUR][1000 genomes]
rs4564921	0.85[EUR][1000 genomes]
rs893704	0.88[EUR][1000 genomes]
rs9816597	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825927	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826668	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139249800-139257400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:139250800-139257400	Enhancers	Brain Cingulate Gyrus	brain
3	chr3:139251200-139257400	Genic enhancers	Fetal Intestine Small	intestine
4	chr3:139251400-139257200	Enhancers	Duodenum Mucosa	Duodenum
5	chr3:139251800-139258600	Enhancers	Fetal Heart	heart
6	chr3:139252000-139257600	Enhancers	Left Ventricle	heart
7	chr3:139252200-139257600	Enhancers	Brain Substantia Nigra	brain
8	chr3:139252800-139257600	Enhancers	Right Ventricle	heart
9	chr3:139252800-139257800	Weak transcription	Psoas Muscle	Psoas
10	chr3:139253000-139258000	Weak transcription	Small Intestine	intestine
11	chr3:139253000-139258200	Enhancers	Spleen	Spleen
12	chr3:139253400-139257400	Genic enhancers	Fetal Stomach	stomach
13	chr3:139253600-139257400	Enhancers	Brain Hippocampus Middle	brain
14	chr3:139253800-139257600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr3:139254600-139257400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:139254800-139257200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:139255000-139257800	Weak transcription	HSMM	muscle
18	chr3:139255000-139258000	Weak transcription	NHLF	lung
19	chr3:139255000-139258200	Weak transcription	Gastric	stomach
20	chr3:139255200-139258000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:139255400-139257200	Weak transcription	Brain Angular Gyrus	brain
22	chr3:139255400-139257600	Weak transcription	Fetal Brain Female	brain
23	chr3:139255400-139257800	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:139255600-139257400	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr3:139255600-139257400	Transcr. at gene 5' and 3'	NH-A	brain
26	chr3:139255800-139257200	Weak transcription	Fetal Brain Male	brain
27	chr3:139255800-139257400	Weak transcription	Lung	lung
28	chr3:139256200-139257200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
29	chr3:139256200-139257400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:139256200-139257800	Weak transcription	Aorta	Aorta
31	chr3:139256200-139257800	Flanking Active TSS	Pancreas	Pancrea
32	chr3:139256200-139258000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:139256200-139258000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:139256400-139257400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr3:139256400-139257400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:139256400-139257400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr3:139256400-139257400	Enhancers	Fetal Intestine Large	intestine
38	chr3:139256400-139257400	Enhancers	Stomach Smooth Muscle	stomach
39	chr3:139256400-139257600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:139256400-139257600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:139256400-139257600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:139256400-139257600	Weak transcription	Liver	Liver
43	chr3:139256400-139257800	ZNF genes & repeats	HMEC	breast
44	chr3:139256400-139258000	ZNF genes & repeats	NHEK	skin
45	chr3:139256600-139257200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:139256600-139257200	Weak transcription	Brain Anterior Caudate	brain
47	chr3:139256600-139257200	Enhancers	Fetal Kidney	kidney
48	chr3:139256600-139257200	Enhancers	Fetal Lung	lung
49	chr3:139256600-139257400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:139256600-139257400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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