Variant report

Variant	rs3861953
Chromosome Location	chr1:173180388-173180389
allele	C/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	FOXA2	chr1:173179870-173180410	HepG2	liver:	n/a	n/a
2	FOXA1	chr1:173179771-173180418	HepG2	liver:	n/a	n/a
3	JUN	chr1:173180003-173180631	HepG2	liver:	n/a	n/a
4	JUND	chr1:173180078-173180466	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:173179352-173180595	HepG2	liver:	n/a	n/a
6	HEY1	chr1:173179271-173180509	HepG2	liver:	n/a	n/a
7	NFIC	chr1:173179815-173180419	HepG2	liver:	n/a	n/a
8	TBP	chr1:173179862-173180396	HepG2	liver:	n/a	n/a
9	MYBL2	chr1:173179291-173180546	HepG2	liver:	n/a	n/a
10	FOXA1	chr1:173179775-173180558	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:173179386-173180722	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:173179498-173180396	HepG2	liver:	n/a	n/a
13	HEY1	chr1:173179794-173180411	HepG2	liver:	n/a	n/a
14	FOXA1	chr1:173179791-173180498	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:173179398-173180488	HepG2	liver:	n/a	n/a
16	EP300	chr1:173179719-173180459	HepG2	liver:	n/a	n/a
17	FOXA1	chr1:173179814-173180410	HepG2	liver:	n/a	n/a
18	MYBL2	chr1:173179331-173180540	HepG2	liver:	n/a	n/a
19	SP1	chr1:173179285-173180484	HepG2	liver:	n/a	chr1:173179548-173179557 chr1:173179860-173179873
20	MBD4	chr1:173179535-173180408	HepG2	liver:	n/a	n/a
21	HNF4A	chr1:173179438-173180494	HepG2	liver:	n/a	chr1:173180060-173180075 chr1:173180086-173180094
22	ARID3A	chr1:173179530-173180564	HepG2	liver:	n/a	n/a
23	MAFK	chr1:173179967-173180464	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TNFSF4	TF binding region

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3850641	0.86[ASN][1000 genomes]
rs45454293	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs844665	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs844666	0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173172000-173181200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:173175200-173193000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:173175600-173182600	Enhancers	Stomach Mucosa	stomach
4	chr1:173175800-173186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:173175800-173193000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:173176600-173180600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:173176800-173180800	Weak transcription	Brain Substantia Nigra	brain
8	chr1:173177000-173181400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:173177000-173181600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:173177200-173180400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:173177600-173183200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:173177800-173195200	Weak transcription	HSMMtube	muscle
13	chr1:173178200-173182600	Enhancers	Fetal Intestine Large	intestine
14	chr1:173178400-173180400	Weak transcription	Fetal Heart	heart
15	chr1:173178600-173181600	Enhancers	Fetal Intestine Small	intestine
16	chr1:173179400-173180400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr1:173179400-173180400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:173179400-173180400	Enhancers	Right Atrium	heart
19	chr1:173179400-173180800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:173179600-173180400	Enhancers	HUVEC	blood vessel
21	chr1:173179600-173180600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr1:173179600-173180800	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:173179800-173180400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:173179800-173180600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
25	chr1:173180000-173180400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:173180000-173180400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:173180000-173180400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr1:173180000-173180400	Enhancers	Right Ventricle	heart
29	chr1:173180000-173180600	Enhancers	Duodenum Mucosa	Duodenum
30	chr1:173180000-173181200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:173180200-173180400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
32	chr1:173180200-173180800	Flanking Active TSS	HepG2	liver

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