Variant report

Variant	rs924262
Chromosome Location	chr3:111262212-111262213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10511298	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916952	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494356	0.85[ASN][1000 genomes]
rs13066911	0.88[ASN][1000 genomes]
rs1391356	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1497990	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1513323	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1603687	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2088468	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276873	0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2399391	0.93[AFR][1000 genomes]
rs6764960	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788797	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721336	0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7616420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7619086	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7628253	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653347	0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs883113	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs968910	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.85[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

No data

Chromatin state (count:38 , 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	chr3:111258600-111265200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111258600-111266800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:111258800-111264200	Weak transcription	Stomach Mucosa	stomach
5	chr3:111258800-111266600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:111259000-111264000	Weak transcription	Fetal Intestine Small	intestine
7	chr3:111260200-111263000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:111260200-111269800	Enhancers	Primary hematopoietic stem cells	blood
9	chr3:111260600-111263400	Active TSS	Thymus	Thymus
10	chr3:111260800-111262400	Active TSS	Primary T cells fromperipheralblood	blood
11	chr3:111260800-111262400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:111260800-111262600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:111260800-111262600	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr3:111260800-111262800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr3:111260800-111263200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr3:111260800-111263200	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr3:111260800-111263400	Active TSS	Duodenum Mucosa	Duodenum
18	chr3:111261000-111262600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:111261000-111263200	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:111261000-111263200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:111261200-111262600	Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr3:111261200-111262800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:111261200-111266400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:111261200-111266800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:111261400-111263200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:111261400-111263200	Active TSS	Fetal Thymus	thymus
27	chr3:111261400-111263800	Enhancers	Primary B cells from peripheral blood	blood
28	chr3:111261400-111266000	Weak transcription	GM12878-XiMat	blood
29	chr3:111261600-111262400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr3:111261800-111262600	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr3:111261800-111262800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:111261800-111264000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:111261800-111265400	Weak transcription	Primary B cells from cord blood	blood
34	chr3:111261800-111266800	Weak transcription	Small Intestine	intestine
35	chr3:111262000-111263200	Flanking Active TSS	Dnd41	blood
36	chr3:111262200-111262400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:111262200-111262800	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr3:111262200-111263200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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