Variant report

Variant	rs2699905
Chromosome Location	chr3:178884337-178884338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178883467..178885785-chr3:178891482..178893959,2	K562	blood:
2	chr3:178884097..178886726-chr3:178940111..178942496,2	K562	blood:
3	chr3:178883567..178885115-chr3:178885473..178887362,2	K562	blood:

Variant related genes	Relation type
ENSG00000201957	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13082485	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13099856	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1517586	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2542298	0.83[ASN][1000 genomes]
rs2677763	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2677764	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2677770	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2699887	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2699891	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2699893	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2699906	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4579062	0.93[GIH][hapmap]
rs4637331	0.80[CEU][hapmap]
rs4955801	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4955807	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs4955810	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs6772028	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs6784495	0.95[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs6790867	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs6793893	0.93[GIH][hapmap]
rs6800015	0.93[GIH][hapmap]
rs6804084	0.80[CEU][hapmap]
rs73187259	0.94[ASN][1000 genomes]
rs7633318	0.93[GIH][hapmap]
rs7639391	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs9968179	0.95[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1003540	chr3:178875803-178886293	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1010571	chr3:178876965-178888153	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv2763744	chr3:178883172-178888165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2699905	EPHB3	cis	cerebellum	SCAN
rs2699905	YEATS2	cis	cerebellum	SCAN
rs2699905	ZMAT3	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178867800-178900200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:178868000-178892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:178868600-178893000	Weak transcription	Aorta	Aorta
4	chr3:178869200-178898000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:178869400-178887200	Weak transcription	Fetal Brain Male	brain
6	chr3:178870800-178896400	Weak transcription	K562	blood
7	chr3:178874800-178888600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:178877400-178897800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:178879000-178885600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:178879200-178891800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:178879400-178892000	Weak transcription	Lung	lung
12	chr3:178879400-178896400	Weak transcription	Right Atrium	heart
13	chr3:178879600-178896400	Weak transcription	Left Ventricle	heart
14	chr3:178880400-178887800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:178881000-178885800	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:178882800-178884600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:178883200-178884800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:178883400-178884400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:178883400-178884400	Weak transcription	Adipose Nuclei	Adipose
20	chr3:178883400-178884600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:178883400-178884800	Enhancers	Fetal Lung	lung
22	chr3:178883400-178887800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:178883600-178884400	Enhancers	Primary B cells from cord blood	blood
24	chr3:178883600-178884400	Weak transcription	Fetal Heart	heart
25	chr3:178883600-178885600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:178883600-178892400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:178883600-178893600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:178883800-178885800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:178883800-178905800	Weak transcription	Fetal Kidney	kidney
30	chr3:178884000-178884600	Enhancers	Brain Germinal Matrix	brain
31	chr3:178884000-178884800	Enhancers	Stomach Mucosa	stomach
32	chr3:178884000-178884800	Flanking Active TSS	GM12878-XiMat	blood
33	chr3:178884000-178885200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:178884200-178884400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:178884200-178884400	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:178884200-178884400	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr3:178884200-178884600	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links