Variant report

Variant	rs998899
Chromosome Location	chr2:167994684-167994685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10451542	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs10497315	0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs1155284	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1155285	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11694517	0.82[ASW][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.87[YRI][hapmap]
rs11888230	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs11893404	0.81[EUR][1000 genomes]
rs11899748	0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11902653	0.93[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs12105903	0.84[ASW][hapmap];0.85[CHD][hapmap];0.94[MEX][hapmap];0.84[YRI][hapmap]
rs12619579	0.81[YRI][hapmap]
rs12692857	0.85[CHD][hapmap];0.94[MEX][hapmap]
rs1346722	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1346723	0.84[ASW][hapmap];0.83[GIH][hapmap]
rs1479592	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes]
rs16852941	0.94[MEX][hapmap];0.82[YRI][hapmap]
rs16853050	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes]
rs16853057	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs16853217	0.83[TSI][hapmap]
rs4000962	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4533448	0.93[CEU][hapmap]
rs55733637	0.80[EUR][1000 genomes]
rs56730065	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6432974	0.89[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6432975	0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6432979	0.95[EUR][1000 genomes]
rs6432984	0.89[ASW][hapmap]
rs66701411	0.85[EUR][1000 genomes]
rs6706173	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs67074513	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6711844	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs6720352	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6720763	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6733384	0.83[LWK][hapmap];0.88[YRI][hapmap]
rs67386767	0.81[EUR][1000 genomes]
rs6742332	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs67726376	0.80[EUR][1000 genomes]
rs73017939	0.83[EUR][1000 genomes]
rs7569147	0.93[CEU][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs7580360	0.85[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap]
rs7586785	0.82[YRI][hapmap]
rs7592671	0.83[YRI][hapmap]
rs7599374	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs7607028	0.82[CHD][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap]
rs988445	0.93[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875376	chr2:167844513-168037489	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs998899	SNX19	trans	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:167989200-167998600	Weak transcription	Left Ventricle	heart
2	chr2:167990200-167995200	Enhancers	NHLF	lung
3	chr2:167990400-167996600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:167991600-167997000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:167992000-167996800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:167992200-167996800	Weak transcription	HSMMtube	muscle
7	chr2:167992200-167999800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:167992400-167996200	Weak transcription	Fetal Heart	heart
9	chr2:167992400-167996600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:167992600-167996800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:167992600-167996800	Weak transcription	NH-A	brain
12	chr2:167992600-167996800	Weak transcription	Osteobl	bone
13	chr2:167992600-167997200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:167993200-167995000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:167993200-167995200	Enhancers	Fetal Lung	lung
16	chr2:167993200-167995600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:167993400-167996800	Weak transcription	HUVEC	blood vessel
18	chr2:167993400-167997000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:167993600-167997200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:167993800-167996200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:167993800-167996600	Weak transcription	HSMM	muscle
22	chr2:167993800-167996800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:167993800-167997000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:167993800-167997000	Weak transcription	Psoas Muscle	Psoas
25	chr2:167993800-167999800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:167994000-167995000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:167994000-167995000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:167994000-167996200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:167994000-167996200	Weak transcription	HMEC	breast
30	chr2:167994200-167996800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:167994200-167996800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:167994400-167996000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:167994400-167996800	Weak transcription	NHDF-Ad	bronchial

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