Variant report

Variant	rs4682496
Chromosome Location	chr3:113290891-113290892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113213756..113215822-chr3:113289553..113292461,2	MCF-7	breast:
2	chr3:113233838..113235537-chr3:113290366..113293108,2	MCF-7	breast:
3	chr3:113286843..113290980-chr3:113291829..113295911,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11929640	1.00[ASW][hapmap];0.85[GIH][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12631929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1567779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1567780	0.88[MKK][hapmap]
rs1567781	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2048624	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271495	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28446408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28530478	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564696	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34842926	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3773691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3896909	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3932276	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41271363	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4560271	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4560272	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682493	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682494	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55941419	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56721892	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62265514	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62265515	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62265518	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62265519	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62265520	0.95[ASN][1000 genomes]
rs62265521	0.95[ASN][1000 genomes]
rs6787428	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72950888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637206	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9816095	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823358	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9844542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854140	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9863703	0.85[GIH][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs9868243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874993	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9879239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985452	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4682496	SIDT1	cis	cerebellum	SCAN
rs4682496	SIDT1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113276800-113294200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:113279200-113300000	Weak transcription	Thymus	Thymus
3	chr3:113280200-113299200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:113280200-113321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:113280400-113304000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:113280600-113302400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:113280600-113314800	Weak transcription	Spleen	Spleen
8	chr3:113281400-113302200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:113281600-113296400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:113281800-113296200	Strong transcription	Primary T cells from cord blood	blood
11	chr3:113283200-113296200	Strong transcription	GM12878-XiMat	blood
12	chr3:113283400-113292200	Strong transcription	Primary B cells from cord blood	blood
13	chr3:113285200-113329800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine
15	chr3:113285400-113294200	Weak transcription	Esophagus	oesophagus
16	chr3:113285600-113292400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:113286000-113316800	Weak transcription	Brain Angular Gyrus	brain
18	chr3:113287000-113291200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:113287000-113292200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:113287200-113301400	Weak transcription	Fetal Thymus	thymus
21	chr3:113287400-113293000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:113287800-113298600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:113287800-113299200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:113288000-113300000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:113288000-113302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:113289400-113291000	Weak transcription	A549	lung
27	chr3:113289600-113293800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:113289600-113294200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:113289800-113291800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:113289800-113299400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:113290000-113296400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:113290000-113296400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:113290600-113291400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:113290600-113292000	Weak transcription	Primary T cells fromperipheralblood	blood

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