Variant report

Variant	rs2899051
Chromosome Location	chr15:42786160-42786161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr15:42786054-42786171	K562	blood:	n/a	n/a
2	SPI1	chr15:42785845-42786353	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42781216..42785618-chr15:42786050..42793334,15	K562	blood:
2	chr15:42785710..42787693-chr15:42866156..42868186,2	K562	blood:
3	chr15:42781216..42785097-chr15:42786050..42789793,8	K562	blood:

Variant related genes	Relation type
SNAP23	TF binding region
ZNF106	TF binding region
ENSG00000103994	Chromatin interaction
ENSG00000092531	Chromatin interaction
ENSG00000159433	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10454039	0.86[EUR][1000 genomes]
rs10518763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10518766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060291	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060293	1.00[ASN][1000 genomes]
rs10851410	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10851411	0.84[EUR][1000 genomes]
rs11022	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070374	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11070376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11631193	0.83[EUR][1000 genomes]
rs11636577	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638208	0.87[EUR][1000 genomes]
rs12324113	0.89[EUR][1000 genomes]
rs12324717	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12903432	0.91[EUR][1000 genomes]
rs12906697	0.86[EUR][1000 genomes]
rs12913324	0.84[EUR][1000 genomes]
rs16973053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973054	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973089	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973091	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973093	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973095	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973097	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973107	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973132	1.00[CHB][hapmap]
rs16973137	1.00[CHB][hapmap]
rs16973148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973155	1.00[CHB][hapmap]
rs16973171	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17695121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17709180	1.00[ASN][1000 genomes]
rs17709377	1.00[ASN][1000 genomes]
rs17766532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1900920	0.80[EUR][1000 genomes]
rs1900921	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241998	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2255995	0.90[EUR][1000 genomes]
rs2412704	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2595939	0.91[EUR][1000 genomes]
rs2595940	0.85[CEU][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs2595941	0.89[EUR][1000 genomes]
rs2617236	0.85[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs28364347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28886308	0.85[EUR][1000 genomes]
rs2899057	0.86[EUR][1000 genomes]
rs2899059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34359922	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34643746	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792942	1.00[ASN][1000 genomes]
rs3986280	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344713	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4573906	0.91[EUR][1000 genomes]
rs4923948	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924684	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924687	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56357092	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56982416	1.00[ASN][1000 genomes]
rs58042601	1.00[ASN][1000 genomes]
rs58641431	1.00[ASN][1000 genomes]
rs59697584	1.00[ASN][1000 genomes]
rs59705032	1.00[ASN][1000 genomes]
rs60380503	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60584955	1.00[ASN][1000 genomes]
rs60812675	1.00[ASN][1000 genomes]
rs61489160	1.00[ASN][1000 genomes]
rs62022317	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7164874	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7165023	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7169615	0.81[EUR][1000 genomes]
rs7178901	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7180483	1.00[ASN][1000 genomes]
rs7182797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73402783	1.00[ASN][1000 genomes]
rs73402785	1.00[ASN][1000 genomes]
rs73404714	1.00[ASN][1000 genomes]
rs73404723	1.00[ASN][1000 genomes]
rs73404730	1.00[ASN][1000 genomes]
rs73404763	1.00[ASN][1000 genomes]
rs73406518	1.00[ASN][1000 genomes]
rs73406534	1.00[ASN][1000 genomes]
rs73406545	1.00[ASN][1000 genomes]
rs74009095	1.00[ASN][1000 genomes]
rs8033412	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034232	0.80[EUR][1000 genomes]
rs8038153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9302112	0.85[CEU][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2899051	SNAP23	cis	parietal	SCAN
rs2899051	MAP1A	cis	parietal	SCAN
rs2899051	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs2899051	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs2899051	CXorf57	trans	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42783400-42787400	Weak transcription	Gastric	stomach
2	chr15:42783600-42786800	Weak transcription	Lung	lung
3	chr15:42783600-42787200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:42783600-42787400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:42783600-42787800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:42783600-42787800	Weak transcription	Spleen	Spleen
7	chr15:42783800-42786800	Weak transcription	Esophagus	oesophagus
8	chr15:42783800-42787000	Enhancers	Primary B cells from peripheral blood	blood
9	chr15:42783800-42787000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:42783800-42787200	Enhancers	Placenta	Placenta
11	chr15:42783800-42787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:42783800-42787400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:42784000-42786200	Weak transcription	NHDF-Ad	bronchial
14	chr15:42784000-42786400	Weak transcription	Liver	Liver
15	chr15:42784000-42786600	Weak transcription	Brain Anterior Caudate	brain
16	chr15:42784000-42786600	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:42784000-42787000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:42784000-42787000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:42784000-42787000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:42784000-42787000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr15:42784000-42787000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr15:42784000-42787000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:42784000-42787000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr15:42784000-42787000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr15:42784000-42787000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:42784000-42787000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:42784000-42787000	Weak transcription	Brain Angular Gyrus	brain
28	chr15:42784000-42787000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:42784000-42787000	Weak transcription	Brain Germinal Matrix	brain
30	chr15:42784000-42787000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:42784000-42787000	Weak transcription	Brain Substantia Nigra	brain
32	chr15:42784000-42787000	Weak transcription	Fetal Brain Female	brain
33	chr15:42784000-42787000	Weak transcription	Fetal Lung	lung
34	chr15:42784000-42787000	Weak transcription	Fetal Stomach	stomach
35	chr15:42784000-42787000	Weak transcription	Right Ventricle	heart
36	chr15:42784000-42787000	Weak transcription	A549	lung
37	chr15:42784000-42787000	Weak transcription	HSMMtube	muscle
38	chr15:42784000-42787000	Enhancers	HUVEC	blood vessel
39	chr15:42784000-42787200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:42784000-42787200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:42784000-42787200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:42784000-42787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:42784000-42787200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:42784000-42787200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:42784000-42787200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:42784200-42786400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:42784200-42786800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:42784200-42786800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:42784200-42787000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:42784200-42787000	Weak transcription	Fetal Intestine Large	intestine

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