Variant report

Variant	rs10489266
Chromosome Location	chr1:173178453-173178454
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	MAFK	chr1:173178218-173178462	HepG2	liver:	n/a	n/a
2	MAX	chr1:173178376-173178470	GM12878	blood:	n/a	n/a
3	JUN	chr1:173178213-173178462	K562	blood:	n/a	n/a

Variant related genes	Relation type
TNFSF4	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10465507	1.00[ASN][1000 genomes]
rs10489268	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10798264	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10912558	1.00[ASN][1000 genomes]
rs10912560	1.00[CHB][hapmap]
rs10912561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11587348	1.00[ASN][1000 genomes]
rs11801818	1.00[ASN][1000 genomes]
rs11806687	1.00[ASN][1000 genomes]
rs11807031	1.00[ASN][1000 genomes]
rs11808060	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12120808	0.82[ASN][1000 genomes]
rs12125395	0.82[ASN][1000 genomes]
rs12138547	0.82[ASN][1000 genomes]
rs12141186	0.82[ASN][1000 genomes]
rs12144635	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs12144665	0.82[ASN][1000 genomes]
rs13343108	1.00[CHB][hapmap]
rs17300347	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17300677	0.82[ASN][1000 genomes]
rs17300754	0.82[ASN][1000 genomes]
rs17346501	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17372309	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs3850641	1.00[YRI][hapmap]
rs4090392	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4113832	1.00[ASN][1000 genomes]
rs4916210	1.00[ASN][1000 genomes]
rs4916314	1.00[ASN][1000 genomes]
rs56074681	1.00[ASN][1000 genomes]
rs57928823	1.00[ASN][1000 genomes]
rs61826345	1.00[ASN][1000 genomes]
rs61828261	1.00[ASN][1000 genomes]
rs61828267	0.82[ASN][1000 genomes]
rs72722845	1.00[ASN][1000 genomes]
rs72722865	0.82[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489266	TNFSF18	cis	cerebellum	SCAN
rs10489266	TNFSF4	cis	cerebellum	SCAN

Chromatin state (count:35 , 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	chr1:173172800-173179400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:173174800-173179400	Enhancers	HepG2	liver
4	chr1:173175200-173179400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:173175200-173179400	Weak transcription	Left Ventricle	heart
6	chr1:173175200-173180000	Weak transcription	Right Ventricle	heart
7	chr1:173175200-173193000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:173175600-173182600	Enhancers	Stomach Mucosa	stomach
9	chr1:173175800-173186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:173175800-173193000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:173176400-173179400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:173176400-173179400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:173176400-173179800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:173176600-173178800	Weak transcription	Ovary	ovary
15	chr1:173176600-173179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:173176600-173179400	Weak transcription	Right Atrium	heart
17	chr1:173176600-173180600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:173176800-173178600	Enhancers	HSMM	muscle
19	chr1:173176800-173180800	Weak transcription	Brain Substantia Nigra	brain
20	chr1:173177000-173178600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:173177000-173179400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:173177000-173179800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:173177000-173181400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:173177000-173181600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:173177200-173179600	Weak transcription	HUVEC	blood vessel
26	chr1:173177200-173180400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:173177600-173178600	Weak transcription	Fetal Intestine Small	intestine
28	chr1:173177600-173178800	Weak transcription	Fetal Thymus	thymus
29	chr1:173177600-173178800	Weak transcription	Dnd41	blood
30	chr1:173177600-173180000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:173177600-173183200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:173177800-173179600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:173177800-173195200	Weak transcription	HSMMtube	muscle
34	chr1:173178200-173182600	Enhancers	Fetal Intestine Large	intestine
35	chr1:173178400-173180400	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links