Variant report

Variant	rs1233462
Chromosome Location	chr19:44759288-44759289
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44751203..44753045-chr19:44757395..44759425,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1233430	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1233431	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233432	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233433	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233434	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233435	0.82[AMR][1000 genomes]
rs1233436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233442	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233443	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1233445	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233446	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233450	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233451	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233452	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233457	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233458	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233460	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233461	0.89[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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233469	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1233471	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1233472	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1233473	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1233474	0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1234839	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234840	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1235163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1237178	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1237179	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs1238786	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347349	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1369100	0.96[EUR][1000 genomes]
rs16978991	0.80[CEU][hapmap]
rs17657025	0.85[CEU][hapmap]
rs2117385	0.81[CEU][hapmap]
rs2117387	0.81[CEU][hapmap]
rs2164112	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2164113	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2168990	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2196185	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2249402	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2446491	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2571076	0.81[CEU][hapmap]
rs2571100	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2571105	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2571106	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2609881	1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2609883	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2609886	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609887	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2609890	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2609892	1.00[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2609898	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2609905	0.87[EUR][1000 genomes]
rs2609906	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2609907	1.00[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs2609909	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2722707	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2722708	1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2722711	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2722715	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2722716	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2722717	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59555311	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6509153	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs874187	1.00[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs898175	1.00[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs898176	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs898177	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs898179	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs984116	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1233462	FLT3LG	cis	parietal	SCAN
rs1233462	NKPD1	cis	cerebellum	SCAN
rs1233462	KLK7	cis	cerebellum	SCAN
rs1233462	AKT1S1	cis	cerebellum	SCAN
rs1233462	IL4I1	cis	parietal	SCAN
rs1233462	ZNF473	cis	cerebellum	SCAN
rs1233462	KLK9	cis	parietal	SCAN
rs1233462	SYT3	cis	cerebellum	SCAN
rs1233462	SNORD33	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44729800-44768600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:44730000-44775600	ZNF genes & repeats	Liver	Liver
3	chr19:44742000-44763800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:44756400-44762600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:44757800-44759400	ZNF genes & repeats	Fetal Lung	lung
6	chr19:44757800-44759400	ZNF genes & repeats	Left Ventricle	heart
7	chr19:44757800-44759400	ZNF genes & repeats	Psoas Muscle	Psoas
8	chr19:44757800-44759600	ZNF genes & repeats	Brain Substantia Nigra	brain
9	chr19:44758000-44759600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
10	chr19:44758000-44759800	Enhancers	HepG2	liver
11	chr19:44758200-44759400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:44758200-44759400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr19:44758200-44759400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
14	chr19:44758400-44759600	ZNF genes & repeats	Ovary	ovary
15	chr19:44758600-44759400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
16	chr19:44759000-44759600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links