Variant report

Variant	rs2570934
Chromosome Location	chr15:100143999-100144000
allele	A/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:39)

rs_ID	r²[population]
rs11633385	0.88[CHB][hapmap]
rs11636728	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2123930	1.00[ASW][hapmap];0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs2439248	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570799	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]
rs2570804	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570805	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570806	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570813	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2570817	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570821	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570822	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570927	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570930	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581464	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581465	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581466	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2581474	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2862871	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863274	0.94[CHB][hapmap];0.80[MEX][hapmap]
rs2863278	0.82[CHB][hapmap]
rs325384	0.89[ASN][1000 genomes]
rs325386	0.89[ASN][1000 genomes]
rs325389	0.90[ASN][1000 genomes]
rs325393	1.00[ASW][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs325396	0.84[ASN][1000 genomes]
rs325397	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs325398	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs325403	0.82[CHD][hapmap]
rs325412	0.88[ASN][1000 genomes]
rs325415	0.90[ASN][1000 genomes]
rs34937961	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35376034	0.86[ASN][1000 genomes]
rs4408523	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56248519	0.86[ASN][1000 genomes]
rs72760522	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72760533	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029296	0.87[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8034889	0.87[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv904558	chr15:100019382-100171684	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv1798883	chr15:100124483-100153969	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2570934	LYSMD4	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100129400-100155200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:100130000-100153000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:100132600-100154800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:100132800-100153200	Weak transcription	HepG2	liver
5	chr15:100133000-100144400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:100133000-100145400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:100133000-100145600	Weak transcription	NH-A	brain
8	chr15:100133000-100153400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:100133000-100155000	Weak transcription	Esophagus	oesophagus
10	chr15:100133000-100157000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:100133000-100159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:100133000-100159200	Weak transcription	A549	lung
13	chr15:100133200-100144200	Weak transcription	HUVEC	blood vessel
14	chr15:100133200-100148000	Weak transcription	Stomach Mucosa	stomach
15	chr15:100133800-100146000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:100135000-100149200	Weak transcription	Pancreas	Pancrea
17	chr15:100135400-100145000	Weak transcription	Aorta	Aorta
18	chr15:100135600-100152000	Weak transcription	HSMMtube	muscle
19	chr15:100135800-100153600	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:100138400-100145400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:100138800-100149200	Weak transcription	Fetal Brain Male	brain
22	chr15:100139000-100153800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:100140000-100153400	Weak transcription	Fetal Intestine Small	intestine
24	chr15:100140200-100145000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:100140600-100145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:100140600-100147200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:100140800-100144800	Weak transcription	NHEK	skin
28	chr15:100140800-100148000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:100140800-100148000	Weak transcription	Fetal Brain Female	brain
30	chr15:100140800-100153400	Weak transcription	Fetal Intestine Large	intestine
31	chr15:100141000-100144000	Weak transcription	Osteobl	bone
32	chr15:100141000-100147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:100141000-100148000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:100141000-100150800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:100141000-100152600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:100141000-100154800	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:100141000-100156600	Weak transcription	Brain Angular Gyrus	brain
38	chr15:100141000-100156800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:100141000-100157200	Weak transcription	Fetal Kidney	kidney
40	chr15:100141200-100150400	Weak transcription	HSMM	muscle
41	chr15:100141200-100152800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:100141200-100154000	Weak transcription	Hela-S3	cervix
43	chr15:100141200-100154000	Weak transcription	NHDF-Ad	bronchial
44	chr15:100141600-100148600	Enhancers	Fetal Heart	heart
45	chr15:100141800-100145000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:100141800-100154200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:100142000-100144000	Strong transcription	Thymus	Thymus
48	chr15:100142000-100153200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:100142200-100144000	Strong transcription	Fetal Muscle Leg	muscle
50	chr15:100142200-100153600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links