Variant report

Variant	rs2276873
Chromosome Location	chr3:111260975-111260976
allele	A/G
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	CHD2	chr3:111260849-111261095	GM12878	blood:	n/a	n/a
2	MAZ	chr3:111260817-111261388	GM12878	blood:	n/a	n/a
3	SPI1	chr3:111260814-111261032	GM12878	blood:	n/a	chr3:111260938-111260947
4	RUNX3	chr3:111260742-111261354	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:111260786-111261108	GM12878	blood:	n/a	n/a
6	TBP	chr3:111260728-111261452	GM12878	blood:	n/a	n/a
7	MXI1	chr3:111260805-111261137	GM12878	blood:	n/a	n/a
8	RCOR1	chr3:111260749-111261273	GM12878	blood:	n/a	n/a
9	EP300	chr3:111260461-111261496	GM12878	blood:	n/a	n/a
10	WRNIP1	chr3:111260858-111261083	GM12878	blood:	n/a	n/a
11	PAX5	chr3:111260831-111261051	GM12878	blood:	n/a	n/a
12	MAX	chr3:111260797-111261299	GM12878	blood:	n/a	n/a
13	EP300	chr3:111260785-111261304	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CD96	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10511298	0.88[CEU][hapmap];0.91[GIH][hapmap]
rs10511299	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10934101	0.94[EUR][1000 genomes]
rs11916952	0.88[CEU][hapmap]
rs12631939	0.81[ASN][1000 genomes]
rs12633539	0.87[ASN][1000 genomes]
rs13087173	0.88[ASN][1000 genomes]
rs13087579	0.88[ASN][1000 genomes]
rs1391356	0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs1391362	0.81[ASN][1000 genomes]
rs1398748	0.83[GIH][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1497990	0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs1513324	0.89[YRI][hapmap]
rs1513325	0.89[YRI][hapmap]
rs1948625	0.81[ASN][1000 genomes]
rs2088468	0.80[EUR][1000 genomes]
rs2173318	0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2221065	0.81[ASN][1000 genomes]
rs4682049	0.91[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs6773012	0.81[ASN][1000 genomes]
rs6793230	0.81[ASN][1000 genomes]
rs7616420	0.88[CEU][hapmap];0.87[GIH][hapmap]
rs7619086	0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs7619313	0.89[YRI][hapmap]
rs7619498	0.85[YRI][hapmap]
rs7628039	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7628253	0.88[EUR][1000 genomes]
rs7653347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924262	0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs9865195	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv3946	chr3:111236035-111283038	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2276873	SLC35A5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111255800-111264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:111257200-111261000	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:111258000-111261200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:111258600-111265200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:111258600-111266800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:111258800-111261000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:111258800-111264200	Weak transcription	Stomach Mucosa	stomach
8	chr3:111258800-111266600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:111259000-111264000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:111260000-111261000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr3:111260000-111261000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:111260000-111261200	Enhancers	NH-A	brain
13	chr3:111260200-111261000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr3:111260200-111261000	Flanking Active TSS	Dnd41	blood
15	chr3:111260200-111261400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:111260200-111263000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:111260200-111269800	Enhancers	Primary hematopoietic stem cells	blood
18	chr3:111260400-111261000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:111260400-111261000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:111260400-111261000	Enhancers	Fetal Lung	lung
21	chr3:111260400-111261200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:111260400-111261400	Enhancers	GM12878-XiMat	blood
23	chr3:111260600-111261200	Enhancers	Primary B cells from cord blood	blood
24	chr3:111260600-111261200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:111260600-111261400	Flanking Active TSS	Fetal Thymus	thymus
26	chr3:111260600-111261800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr3:111260600-111263400	Active TSS	Thymus	Thymus
28	chr3:111260800-111261000	Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr3:111260800-111261000	Weak transcription	Small Intestine	intestine
30	chr3:111260800-111261000	Enhancers	NHEK	skin
31	chr3:111260800-111261200	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:111260800-111262200	Active TSS	Primary T cells from cord blood	blood
33	chr3:111260800-111262200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:111260800-111262400	Active TSS	Primary T cells fromperipheralblood	blood
35	chr3:111260800-111262400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:111260800-111262600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:111260800-111262600	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr3:111260800-111262800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr3:111260800-111263200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr3:111260800-111263200	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr3:111260800-111263400	Active TSS	Duodenum Mucosa	Duodenum

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