Variant report

Variant	rs2497339
Chromosome Location	chr10:94606337-94606338
allele	A/C
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	chr10:94605616-94609119	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:94351135..94353608-chr10:94605711..94608172,2	K562	blood:
2	chr10:94448193..94452899-chr10:94604769..94609293,6	K562	blood:
3	chr10:94604476..94607331-chr10:94608009..94611387,4	K562	blood:

Variant related genes	Relation type
EXOC6	TF binding region
ENSG00000138160	Chromatin interaction
ENSG00000152804	Chromatin interaction
ENSG00000138190	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1033976	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466167	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736071	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736072	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10748586	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786057	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187183	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1326329	0.81[EUR][1000 genomes]
rs1326331	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326332	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409387	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536329	0.80[EUR][1000 genomes]
rs1960367	0.81[AMR][1000 genomes]
rs2025730	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094232	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148361	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182451	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246370	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246382	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246701	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250393	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422070	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422072	0.88[CEU][hapmap];0.93[GIH][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488062	1.00[ASN][1000 genomes]
rs2490732	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490733	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490740	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490742	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490744	1.00[ASN][1000 genomes]
rs2497322	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497323	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497324	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497326	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497327	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497331	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497348	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497350	1.00[ASN][1000 genomes]
rs4517429	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933241	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933242	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933749	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933752	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583846	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583848	0.82[EUR][1000 genomes]
rs7069070	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7070025	0.88[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078376	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082382	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089179	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477130	0.81[EUR][1000 genomes]
rs7893270	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894145	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897839	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7909191	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909581	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913340	0.84[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs7914859	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835250	0.81[EUR][1000 genomes]
rs860668	0.81[EUR][1000 genomes]
rs9419746	1.00[ASN][1000 genomes]
rs9633695	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973733	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980204	0.81[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2497339	NOC3L	cis	parietal	SCAN
rs2497339	EXOC6	cis	parietal	SCAN
rs2497339	CEP55	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94596800-94607800	Weak transcription	HSMMtube	muscle
2	chr10:94598600-94607200	Weak transcription	Primary T cells from cord blood	blood
3	chr10:94599400-94607200	Weak transcription	Osteobl	bone
4	chr10:94599400-94607400	Weak transcription	Spleen	Spleen
5	chr10:94599600-94606600	Weak transcription	Lung	lung
6	chr10:94599600-94607600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:94600600-94607800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:94602600-94607600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr10:94602800-94607400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr10:94603000-94607000	Weak transcription	Fetal Intestine Large	intestine
11	chr10:94603000-94607000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr10:94603200-94606400	Weak transcription	Hela-S3	cervix
13	chr10:94603200-94607200	Weak transcription	Liver	Liver
14	chr10:94603200-94607400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr10:94603200-94607400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:94603400-94607200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:94603400-94607200	Weak transcription	A549	lung
18	chr10:94603400-94607400	Weak transcription	Adipose Nuclei	Adipose
19	chr10:94604000-94606800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr10:94604200-94607200	Weak transcription	Placenta	Placenta
21	chr10:94604200-94607400	Weak transcription	Fetal Muscle Leg	muscle
22	chr10:94604200-94607400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:94604200-94607600	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:94605200-94606800	Strong transcription	K562	blood
25	chr10:94605400-94608000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr10:94605600-94606600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr10:94605600-94606600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:94605600-94606600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:94605600-94607600	Enhancers	Primary B cells from peripheral blood	blood
30	chr10:94605800-94606600	Flanking Active TSS	GM12878-XiMat	blood
31	chr10:94605800-94606800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr10:94605800-94607200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr10:94605800-94607200	Genic enhancers	HUVEC	blood vessel
34	chr10:94605800-94607400	Enhancers	HepG2	liver
35	chr10:94606000-94607200	Enhancers	Primary B cells from cord blood	blood
36	chr10:94606200-94606400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:94606200-94607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr10:94606200-94607400	Weak transcription	Fetal Thymus	thymus
39	chr10:94606200-94607800	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links