Variant report

Variant	rs10798649
Chromosome Location	chr1:179022650-179022651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179015639..179017468-chr1:179021224..179023269,2	MCF-7	breast:
2	chr1:178989406..178991304-chr1:179020860..179022775,2	MCF-7	breast:
3	chr1:179019848..179022716-chr1:179024640..179027118,2	MCF-7	breast:
4	chr1:179022260..179024212-chr1:179026385..179028416,3	MCF-7	breast:
5	chr1:178985568..178988566-chr1:179021410..179023796,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10798650	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798651	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10913682	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12021551	0.80[AMR][1000 genomes]
rs1220	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12743735	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2025584	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3753533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766626	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766628	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3820163	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4297249	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4322196	0.87[AMR][1000 genomes]
rs4360490	0.81[AMR][1000 genomes]
rs4652348	0.81[JPT][hapmap]
rs4652351	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61823786	0.88[EUR][1000 genomes]
rs6425512	0.81[JPT][hapmap]
rs6425513	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7515519	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526438	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7544801	0.81[JPT][hapmap]
rs7549040	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912758	0.87[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9283394	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9725887	0.83[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs9727621	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9727648	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10798649	FAM20B	cis	parietal	SCAN
rs10798649	RALGPS2	cis	parietal	SCAN
rs10798649	GPR52	cis	parietal	SCAN
rs10798649	ABL2	cis	parietal	SCAN
rs10798649	FAM20B	cis	cerebellum	SCAN
rs10798649	TOR3A	cis	Artery Tibial	GTEx
rs10798649	TOR3A	cis	multi-tissue	Pritchard
rs10798649	FAM20B	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178998400-179027400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179003800-179025800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:179004200-179024200	Weak transcription	Liver	Liver
4	chr1:179004400-179024200	Weak transcription	Fetal Kidney	kidney
5	chr1:179004800-179024600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:179006000-179024200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:179006400-179024800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:179006400-179032400	Weak transcription	Esophagus	oesophagus
9	chr1:179006800-179024200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:179007000-179024200	Weak transcription	HUVEC	blood vessel
11	chr1:179007600-179024200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:179008000-179033000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:179008400-179023600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:179008400-179033000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:179008400-179041000	Weak transcription	Small Intestine	intestine
16	chr1:179008600-179023600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:179008600-179023600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:179008600-179024200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:179008600-179024400	Weak transcription	Hela-S3	cervix
20	chr1:179008600-179033000	Weak transcription	Brain Angular Gyrus	brain
21	chr1:179008600-179035000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:179008600-179049800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:179008600-179049800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:179008800-179024400	Weak transcription	NHDF-Ad	bronchial
25	chr1:179008800-179024800	Weak transcription	HMEC	breast
26	chr1:179009400-179033000	Weak transcription	Gastric	stomach
27	chr1:179009600-179050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:179011600-179023600	Weak transcription	Dnd41	blood
29	chr1:179011600-179025400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:179011800-179024800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:179011800-179025200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:179012000-179025200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:179012200-179024000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:179012200-179033000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:179012400-179025800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:179012600-179024200	Weak transcription	Fetal Thymus	thymus
37	chr1:179012600-179027600	Weak transcription	Lung	lung
38	chr1:179013000-179023800	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:179013200-179023600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:179013200-179027400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:179013200-179027400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:179013200-179032600	Weak transcription	GM12878-XiMat	blood
43	chr1:179013400-179025000	Weak transcription	Fetal Lung	lung
44	chr1:179013400-179030200	Weak transcription	Fetal Intestine Small	intestine
45	chr1:179013400-179030400	Weak transcription	Fetal Stomach	stomach
46	chr1:179013400-179033200	Weak transcription	Thymus	Thymus
47	chr1:179013800-179023800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:179013800-179024800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:179014200-179024000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:179014200-179024200	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links