Variant report

Variant	rs13067967
Chromosome Location	chr3:113265215-113265216
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113232632..113237183-chr3:113263393..113272581,15	MCF-7	breast:
2	chr3:113219243..113222191-chr3:113264588..113266583,2	MCF-7	breast:
3	chr3:113264597..113268411-chr3:113270878..113272522,4	MCF-7	breast:
4	chr3:113231532..113235670-chr3:113264578..113267346,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10511326	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13065651	0.87[EUR][1000 genomes]
rs13066742	0.85[ASN][1000 genomes]
rs13074313	0.81[AMR][1000 genomes]
rs13083453	0.93[EUR][1000 genomes]
rs13086266	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs13087452	0.85[ASN][1000 genomes]
rs13098166	0.85[ASN][1000 genomes]
rs1486894	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1486897	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1552432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16861158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1872747	0.82[ASN][1000 genomes]
rs2399479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34049435	0.92[EUR][1000 genomes]
rs34056827	0.87[EUR][1000 genomes]
rs34286076	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34680203	0.87[EUR][1000 genomes]
rs34844841	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35274817	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35278902	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35765657	0.87[EUR][1000 genomes]
rs35860985	0.85[ASN][1000 genomes]
rs36054418	0.85[ASN][1000 genomes]
rs3732803	0.84[ASN][1000 genomes]
rs4425226	0.85[ASN][1000 genomes]
rs4484165	0.85[ASN][1000 genomes]
rs60279293	0.93[EUR][1000 genomes]
rs61366244	0.87[EUR][1000 genomes]
rs6438149	0.82[ASN][1000 genomes]
rs6438156	0.85[ASN][1000 genomes]
rs6438157	0.85[ASN][1000 genomes]
rs6438158	0.92[ASN][1000 genomes]
rs6438159	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6438161	0.93[ASN][1000 genomes]
rs66866534	0.92[EUR][1000 genomes]
rs67211112	0.93[ASN][1000 genomes]
rs6766615	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6768648	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6768979	0.85[ASN][1000 genomes]
rs6769516	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6773497	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6783965	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6786974	0.82[ASN][1000 genomes]
rs6787026	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6798938	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6799610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs722392	0.93[ASN][1000 genomes]
rs7613546	0.93[ASN][1000 genomes]
rs7622740	0.85[ASN][1000 genomes]
rs7631082	0.85[ASN][1000 genomes]
rs7631138	0.88[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs869342	0.93[ASN][1000 genomes]
rs869343	0.93[ASN][1000 genomes]
rs9808893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9814395	0.82[ASN][1000 genomes]
rs9825827	0.82[ASN][1000 genomes]
rs9835848	0.82[ASN][1000 genomes]
rs9836396	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9839921	0.85[ASN][1000 genomes]
rs9844447	0.85[ASN][1000 genomes]
rs9872168	0.93[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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13067967	SIDT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113255400-113278800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:113255600-113274800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:113255600-113278400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:113256000-113279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:113257200-113265800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:113257200-113277400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:113257200-113283400	Weak transcription	Primary B cells from cord blood	blood
8	chr3:113258400-113267600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:113261000-113267400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:113261200-113266800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:113261200-113276200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:113262400-113266400	Weak transcription	Thymus	Thymus
13	chr3:113262400-113272200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:113262600-113278800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:113263600-113270000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:113263800-113273000	Weak transcription	Primary T cells from cord blood	blood
17	chr3:113264400-113265400	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:113264400-113266800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr3:113264800-113265800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:113265000-113265600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr3:113265000-113271600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:113265200-113265600	Active TSS	GM12878-XiMat	blood
23	chr3:113265200-113265800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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