Variant report

Variant	rs2570799
Chromosome Location	chr15:100220441-100220442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11633385	0.81[CHB][hapmap]
rs11636728	0.91[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2123930	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2439248	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570804	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2570805	0.91[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2570806	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2570813	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570817	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570821	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2570822	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570927	0.91[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2570930	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570934	1.00[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581464	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581465	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581466	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2581474	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2862871	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2863274	0.89[CHB][hapmap];0.87[MEX][hapmap]
rs325384	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325386	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325389	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs325393	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325396	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs325397	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325398	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325412	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs325415	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34937961	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4408523	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72760522	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72760533	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8029296	0.95[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8034889	0.82[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904559	chr15:100174907-100255046	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv904562	chr15:100214935-100237682	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2570799	LYSMD4	cis	parietal	SCAN
rs2570799	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100159000-100253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100171200-100232800	Weak transcription	Esophagus	oesophagus
3	chr15:100171200-100248800	Weak transcription	Gastric	stomach
4	chr15:100172000-100230800	Weak transcription	Stomach Mucosa	stomach
5	chr15:100179200-100232600	Weak transcription	Colonic Mucosa	Colon
6	chr15:100181800-100232800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:100190600-100222600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:100192000-100230400	Weak transcription	NHLF	lung
9	chr15:100193000-100229000	Weak transcription	Lung	lung
10	chr15:100199800-100232600	Weak transcription	Right Ventricle	heart
11	chr15:100200800-100221600	Weak transcription	Psoas Muscle	Psoas
12	chr15:100209800-100224400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:100209800-100232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:100210800-100220600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:100210800-100223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:100211800-100232200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:100212000-100221800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:100212800-100223800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:100212800-100240000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:100213000-100232600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:100213200-100250800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:100213400-100221400	Weak transcription	Aorta	Aorta
23	chr15:100213400-100226400	Weak transcription	Fetal Brain Male	brain
24	chr15:100213400-100232600	Weak transcription	Pancreas	Pancrea
25	chr15:100213600-100243400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr15:100214400-100220600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:100214400-100223200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:100214400-100223400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:100214400-100224200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr15:100215000-100224600	Strong transcription	Liver	Liver
31	chr15:100215600-100226400	Weak transcription	HepG2	liver
32	chr15:100215800-100222400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:100215800-100223000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:100215800-100223400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:100215800-100230800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:100216000-100221800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:100216000-100222400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:100216000-100222800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:100216000-100223800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:100216000-100224600	Weak transcription	Brain Germinal Matrix	brain
41	chr15:100216000-100224600	Weak transcription	Brain Substantia Nigra	brain
42	chr15:100216200-100222200	Weak transcription	Brain Angular Gyrus	brain
43	chr15:100216200-100222600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:100216200-100222800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:100216200-100226400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:100216200-100229800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:100216200-100230200	Weak transcription	HMEC	breast
48	chr15:100216200-100232600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr15:100216200-100233000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr15:100216400-100222400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links