Variant report

Variant	rs3746733
Chromosome Location	chr20:23349749-23349750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23345633..23349899-chr20:23400647..23404181,5	K562	blood:
2	chr20:23345633..23349899-chr20:23400854..23404181,4	K562	blood:

Variant related genes	Relation type
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1076776	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12625160	0.89[JPT][hapmap]
rs12625164	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12625999	0.89[JPT][hapmap]
rs12626013	0.89[JPT][hapmap]
rs1419008	1.00[LWK][hapmap]
rs17757228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757442	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17830281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936011	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1984279	0.90[LWK][hapmap]
rs2277765	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2281428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2281434	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34648279	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3736755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3746737	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3761274	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3761275	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3827085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827086	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55851398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56094936	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56334525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036423	0.84[JPT][hapmap]
rs6036424	0.84[JPT][hapmap]
rs6048803	0.89[JPT][hapmap]
rs6106669	0.84[JPT][hapmap]
rs6114094	0.89[JPT][hapmap]
rs6114142	0.84[JPT][hapmap]
rs6114144	0.84[JPT][hapmap]
rs6132599	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6132606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132609	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6132610	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132617	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132621	0.89[JPT][hapmap]
rs6132622	0.89[JPT][hapmap]
rs6132623	0.89[JPT][hapmap]
rs6132631	0.84[JPT][hapmap]
rs6137901	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137914	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137937	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137941	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137948	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137950	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137951	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137957	0.89[JPT][hapmap]
rs6137959	0.89[JPT][hapmap]
rs6137961	0.89[JPT][hapmap]
rs6137975	0.84[JPT][hapmap]
rs761722	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8183135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3746733	NXT1	cis	lymphoblastoid	seeQTL
rs3746733	NXT1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23342400-23352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:23344400-23350200	Weak transcription	Fetal Kidney	kidney
4	chr20:23344600-23354200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:23344800-23362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr20:23345000-23361800	Strong transcription	Fetal Thymus	thymus
7	chr20:23345000-23362000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr20:23345000-23362600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr20:23346400-23349800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr20:23346400-23350000	Weak transcription	Aorta	Aorta
11	chr20:23346600-23349800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:23346600-23363200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr20:23346800-23349800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr20:23346800-23349800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr20:23346800-23349800	Weak transcription	Gastric	stomach
16	chr20:23346800-23349800	Weak transcription	Ovary	ovary
17	chr20:23346800-23349800	Weak transcription	Pancreas	Pancrea
18	chr20:23346800-23349800	Genic enhancers	Osteobl	bone
19	chr20:23346800-23350000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr20:23346800-23350000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr20:23346800-23350000	Weak transcription	Esophagus	oesophagus
22	chr20:23346800-23350000	Weak transcription	Lung	lung
23	chr20:23346800-23350400	Weak transcription	Fetal Brain Male	brain
24	chr20:23346800-23350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr20:23346800-23362600	Weak transcription	Right Atrium	heart
26	chr20:23347000-23349800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr20:23347000-23350000	Weak transcription	Fetal Stomach	stomach
28	chr20:23347000-23350200	Weak transcription	Fetal Intestine Small	intestine
29	chr20:23347200-23362400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr20:23347400-23362000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr20:23347600-23349800	Weak transcription	Spleen	Spleen
32	chr20:23347600-23350000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr20:23347600-23355200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr20:23347600-23358600	Strong transcription	Primary T cells from cord blood	blood
35	chr20:23347800-23349800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr20:23347800-23349800	Weak transcription	Hela-S3	cervix
37	chr20:23347800-23350000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr20:23347800-23362000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr20:23347800-23362200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr20:23347800-23362600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr20:23348000-23349800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr20:23348000-23349800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr20:23348000-23350000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr20:23348000-23350000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr20:23348000-23350000	Weak transcription	Brain Germinal Matrix	brain
46	chr20:23348000-23351000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr20:23348000-23353000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr20:23348000-23374200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr20:23348200-23349800	Weak transcription	Brain Substantia Nigra	brain
50	chr20:23348200-23350200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links