Variant report

Variant	rs10935331
Chromosome Location	chr3:139256732-139256733
allele	C/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	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	TCF12	chr3:139255908-139256743	SK-N-SH	brain:	n/a	n/a
5	KAP1	chr3:139255423-139256797	HEK293	kidney:	n/a	chr3:139256358-139256367 chr3:139256355-139256364
6	EP300	chr3:139251629-139259175	SK-N-SH	brain:	n/a	chr3:139256357-139256366 chr3:139253631-139253641 chr3:139252024-139252040 chr3:139256356-139256365
7	SIN3AK20	chr3:139256022-139258994	HCT-116	colon:	n/a	n/a
8	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
9	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
10	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
11	CBX3	chr3:139256018-139258020	HCT-116	colon:	n/a	n/a
12	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
13	SP1	chr3:139255938-139258057	HCT-116	colon:	n/a	chr3:139256874-139256887
14	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
15	SP1	chr3:139255901-139258032	HCT-116	colon:	n/a	chr3:139256874-139256887

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139251496..139253555-chr3:139254279..139256942,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248932	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs167188	0.89[EUR][1000 genomes]
rs176990	1.00[CEU][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs190910	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2071387	0.81[CHB][hapmap]
rs211586	0.96[EUR][1000 genomes]
rs295495	0.87[LWK][hapmap]
rs295497	0.90[ASN][1000 genomes]
rs295498	0.93[ASN][1000 genomes]
rs295501	0.86[EUR][1000 genomes]
rs3772881	0.89[ASW][hapmap]
rs4564921	0.85[EUR][1000 genomes]
rs6797111	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893704	0.92[CEU][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9816597	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825927	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826668	0.90[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:68 , 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	chr3:139250600-139256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:139250800-139257400	Enhancers	Brain Cingulate Gyrus	brain
4	chr3:139251200-139257400	Genic enhancers	Fetal Intestine Small	intestine
5	chr3:139251400-139257200	Enhancers	Duodenum Mucosa	Duodenum
6	chr3:139251800-139258600	Enhancers	Fetal Heart	heart
7	chr3:139252000-139257600	Enhancers	Left Ventricle	heart
8	chr3:139252200-139257600	Enhancers	Brain Substantia Nigra	brain
9	chr3:139252800-139257600	Enhancers	Right Ventricle	heart
10	chr3:139252800-139257800	Weak transcription	Psoas Muscle	Psoas
11	chr3:139253000-139258000	Weak transcription	Small Intestine	intestine
12	chr3:139253000-139258200	Enhancers	Spleen	Spleen
13	chr3:139253400-139257400	Genic enhancers	Fetal Stomach	stomach
14	chr3:139253600-139257400	Enhancers	Brain Hippocampus Middle	brain
15	chr3:139253800-139257600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:139254400-139256800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:139254600-139256800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:139254600-139257400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:139254800-139256800	Weak transcription	Esophagus	oesophagus
20	chr3:139254800-139257200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:139255000-139257800	Weak transcription	HSMM	muscle
22	chr3:139255000-139258000	Weak transcription	NHLF	lung
23	chr3:139255000-139258200	Weak transcription	Gastric	stomach
24	chr3:139255200-139258000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:139255400-139257200	Weak transcription	Brain Angular Gyrus	brain
26	chr3:139255400-139257600	Weak transcription	Fetal Brain Female	brain
27	chr3:139255400-139257800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:139255600-139256800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:139255600-139257400	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr3:139255600-139257400	Transcr. at gene 5' and 3'	NH-A	brain
31	chr3:139255800-139257200	Weak transcription	Fetal Brain Male	brain
32	chr3:139255800-139257400	Weak transcription	Lung	lung
33	chr3:139256000-139256800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr3:139256200-139256800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:139256200-139257000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
36	chr3:139256200-139257200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
37	chr3:139256200-139257400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:139256200-139257800	Weak transcription	Aorta	Aorta
39	chr3:139256200-139257800	Flanking Active TSS	Pancreas	Pancrea
40	chr3:139256200-139258000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr3:139256200-139258000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:139256400-139256800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
43	chr3:139256400-139256800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:139256400-139256800	Enhancers	Placenta Amnion	Placenta Amnion
45	chr3:139256400-139257000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr3:139256400-139257000	Flanking Active TSS	HSMMtube	muscle
47	chr3:139256400-139257400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr3:139256400-139257400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:139256400-139257400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr3:139256400-139257400	Enhancers	Fetal Intestine Large	intestine

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