Variant report

Variant	rs3820163
Chromosome Location	chr1:179041011-179041012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179002539..179004928-chr1:179039985..179042025,2	K562	blood:
2	chr1:178994812..178996811-chr1:179040582..179043210,2	MCF-7	breast:
3	chr1:178994514..178996787-chr1:179040850..179044332,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116199	Chromatin interaction
ENSG00000232750	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10798649	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]
rs10798650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798651	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913682	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12021551	0.85[AMR][1000 genomes]
rs1220	1.00[ASW][hapmap];0.80[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12743735	0.81[ASN][1000 genomes]
rs2025584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753533	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766628	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4297249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4322196	0.82[AMR][1000 genomes]
rs4360490	0.80[AMR][1000 genomes]
rs4652348	0.81[JPT][hapmap]
rs4652351	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6425512	0.81[JPT][hapmap]
rs6425513	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7515519	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7526438	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7544801	0.81[JPT][hapmap]
rs7549040	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs912758	0.91[CEU][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9283394	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9725887	0.87[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9727621	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727648	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3820163	FAM20B	cis	cerebellum	SCAN
rs3820163	RALGPS2	cis	parietal	SCAN
rs3820163	TOR3A	cis	multi-tissue	Pritchard
rs3820163	TOR3A	cis	Artery Tibial	GTEx
rs3820163	FAM20B	cis	lymphoblastoid	seeQTL
rs3820163	ABL2	cis	parietal	SCAN
rs3820163	FAM20B	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179008600-179049800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:179008600-179049800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:179009600-179050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:179025000-179050200	Weak transcription	HUVEC	blood vessel
5	chr1:179025400-179050600	Weak transcription	Fetal Brain Male	brain
6	chr1:179025600-179050000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:179025600-179050400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:179025800-179050200	Weak transcription	Fetal Heart	heart
9	chr1:179027800-179042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:179027800-179050600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:179028600-179050000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:179028600-179050600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:179029600-179043200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:179032600-179043200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:179032600-179043200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:179032800-179041600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:179032800-179043600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:179033000-179041800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:179033000-179043600	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:179033800-179042800	Weak transcription	HMEC	breast
21	chr1:179033800-179050000	Weak transcription	Esophagus	oesophagus
22	chr1:179034000-179050000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:179034200-179050000	Weak transcription	Colonic Mucosa	Colon
24	chr1:179034200-179050000	Weak transcription	Fetal Kidney	kidney
25	chr1:179035000-179042200	Weak transcription	Psoas Muscle	Psoas
26	chr1:179035400-179050000	Weak transcription	Fetal Lung	lung
27	chr1:179036000-179046800	Weak transcription	NHLF	lung
28	chr1:179036200-179041200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:179036200-179046400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:179036200-179049200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:179036200-179050200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:179036200-179050800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:179036400-179041200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:179036400-179041800	Weak transcription	HSMMtube	muscle
35	chr1:179036400-179049200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:179036400-179050000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:179036400-179050200	Weak transcription	Stomach Mucosa	stomach
38	chr1:179036400-179050400	Weak transcription	Right Ventricle	heart
39	chr1:179036600-179041600	Strong transcription	Fetal Stomach	stomach
40	chr1:179037000-179041400	Weak transcription	Brain Germinal Matrix	brain
41	chr1:179037000-179042400	Strong transcription	Ovary	ovary
42	chr1:179038400-179041200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:179038400-179042200	Weak transcription	A549	lung
44	chr1:179038400-179042800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:179038400-179049800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:179038400-179049800	Weak transcription	HepG2	liver
47	chr1:179038600-179041200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:179038600-179050000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:179039600-179045200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:179040000-179041800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links