Variant report

Variant	rs17392948
Chromosome Location	chr3:99754498-99754499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99753937..99756360-chr3:99757732..99759441,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10049383	0.93[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1017968	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1021103	0.93[CEU][hapmap]
rs10212525	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1021341	0.87[CEU][hapmap];0.81[GIH][hapmap];0.83[AMR][1000 genomes]
rs10511177	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs11537816	0.93[GIH][hapmap]
rs13064704	0.93[CEU][hapmap];0.90[AMR][1000 genomes]
rs13069311	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13093838	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13323143	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs1489816	0.86[ASW][hapmap];0.93[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes]
rs1688766	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.88[MKK][hapmap]
rs17379739	0.81[EUR][1000 genomes]
rs17393059	0.83[AMR][1000 genomes]
rs2291494	0.90[AMR][1000 genomes]
rs2291495	0.90[AMR][1000 genomes]
rs28503408	0.83[AMR][1000 genomes]
rs28714363	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28870092	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34922392	0.83[AMR][1000 genomes]
rs34996634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35154249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35521705	0.84[EUR][1000 genomes]
rs35669453	0.90[AMR][1000 genomes]
rs35844878	0.90[AMR][1000 genomes]
rs35885423	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4075038	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.83[MKK][hapmap]
rs4279135	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4361315	0.86[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap]
rs4571265	0.86[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.80[EUR][1000 genomes]
rs4928149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4928234	0.82[EUR][1000 genomes]
rs62285461	0.90[AMR][1000 genomes]
rs62285462	0.90[AMR][1000 genomes]
rs62285471	0.90[AMR][1000 genomes]
rs62285473	0.90[AMR][1000 genomes]
rs62285478	0.81[AMR][1000 genomes]
rs6790535	0.87[CEU][hapmap];0.81[GIH][hapmap];0.83[AMR][1000 genomes]
rs6790877	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs6799379	0.87[CEU][hapmap];0.81[GIH][hapmap];0.83[AMR][1000 genomes]
rs6802422	0.86[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes]
rs6806178	0.87[CEU][hapmap];0.81[GIH][hapmap];0.84[AMR][1000 genomes]
rs6807176	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs704582	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.83[MKK][hapmap]
rs71313585	0.87[AMR][1000 genomes]
rs7610486	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7616988	0.87[CEU][hapmap];0.81[GIH][hapmap]
rs7620228	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7627991	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs793499	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.83[MKK][hapmap]
rs923470	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs923471	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9289985	0.86[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap]
rs9810235	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9814359	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs9815439	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs9823908	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9828079	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9832186	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9833888	0.86[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9833980	0.86[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes]
rs9837602	0.93[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs9841186	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9851645	0.93[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9852435	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9853823	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9854260	0.93[CEU][hapmap];0.96[GIH][hapmap];0.81[AMR][1000 genomes]
rs9860290	0.84[ASW][hapmap];0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9864437	0.86[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes]
rs9873709	0.87[CEU][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs9873878	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9875640	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs9875664	0.81[EUR][1000 genomes]
rs9875878	0.86[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap]
rs9878931	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17392948	LRRC37A	trans	brain	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
5	chr3:99742400-99766400	Weak transcription	Aorta	Aorta
6	chr3:99743800-99759200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:99744200-99759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:99746000-99758800	Weak transcription	Left Ventricle	heart
9	chr3:99746600-99762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:99749000-99759400	Weak transcription	Stomach Mucosa	stomach
11	chr3:99750600-99757800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:99751000-99759200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:99751400-99761000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:99751800-99755600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:99752200-99759400	Weak transcription	Small Intestine	intestine
16	chr3:99752200-99774600	Weak transcription	Gastric	stomach
17	chr3:99752400-99757400	Weak transcription	Pancreas	Pancrea
18	chr3:99752400-99759000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:99753000-99758400	Weak transcription	HUVEC	blood vessel
20	chr3:99753200-99754600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:99753200-99758400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:99753200-99758800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:99753200-99759600	Weak transcription	Ovary	ovary
24	chr3:99753200-99761600	Weak transcription	Psoas Muscle	Psoas
25	chr3:99753400-99758800	Weak transcription	Fetal Stomach	stomach
26	chr3:99753400-99758800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:99753400-99758800	Weak transcription	NHDF-Ad	bronchial
28	chr3:99753600-99758000	Weak transcription	HSMM	muscle
29	chr3:99753600-99758800	Weak transcription	Osteobl	bone
30	chr3:99753600-99759000	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:99753600-99759000	Weak transcription	Fetal Kidney	kidney
32	chr3:99753600-99759000	Weak transcription	HMEC	breast
33	chr3:99753600-99759200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:99753800-99755000	Weak transcription	HSMMtube	muscle
35	chr3:99753800-99758800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:99753800-99759200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:99753800-99759200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:99754000-99757600	Weak transcription	Fetal Intestine Large	intestine
39	chr3:99754000-99759200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:99754200-99754800	Weak transcription	HepG2	liver
41	chr3:99754400-99759600	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links