Variant report

Variant	rs716704
Chromosome Location	chr12:29257225-29257226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29255547..29258096-chr12:29276125..29278955,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10734770	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743643	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11049992	0.86[EUR][1000 genomes]
rs1121577	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11502454	1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12298186	0.86[EUR][1000 genomes]
rs12302010	0.89[EUR][1000 genomes]
rs12302231	0.88[EUR][1000 genomes]
rs12304386	0.89[EUR][1000 genomes]
rs12305429	1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12309591	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12311115	0.92[EUR][1000 genomes]
rs12320204	0.90[EUR][1000 genomes]
rs1353460	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1390542	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17449204	0.88[EUR][1000 genomes]
rs17449238	0.88[EUR][1000 genomes]
rs1826801	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1865763	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1865764	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2196479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2349971	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28544897	0.92[EUR][1000 genomes]
rs3940535	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930849	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930850	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930852	0.91[ASN][1000 genomes]
rs4931154	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59113616	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60329521	0.98[EUR][1000 genomes]
rs6487757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487764	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66487137	0.89[EUR][1000 genomes]
rs66712682	0.89[EUR][1000 genomes]
rs67060812	0.89[EUR][1000 genomes]
rs67087836	0.89[EUR][1000 genomes]
rs67287552	0.89[EUR][1000 genomes]
rs67563394	0.89[EUR][1000 genomes]
rs67760969	0.92[EUR][1000 genomes]
rs7304088	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73061737	0.89[EUR][1000 genomes]
rs73061745	0.89[EUR][1000 genomes]
rs7315912	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316030	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73254758	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73254786	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73268857	0.88[EUR][1000 genomes]
rs73268858	0.88[EUR][1000 genomes]
rs73273123	0.90[EUR][1000 genomes]
rs7964313	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2758301	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759888	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs716704	IFLTD1	cis	parietal	SCAN
rs716704	ERGIC2	cis	parietal	SCAN
rs716704	BICD1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29255400-29257800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:29255800-29257400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:29255800-29257400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr12:29255800-29257400	Flanking Active TSS	Dnd41	blood
5	chr12:29255800-29257600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:29256000-29257400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr12:29256000-29257400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:29256400-29257800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr12:29256800-29257400	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr12:29256800-29257400	Enhancers	Small Intestine	intestine
11	chr12:29256800-29257600	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:29256800-29257800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:29256800-29259200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:29256800-29259600	Enhancers	Primary hematopoietic stem cells	blood
15	chr12:29257000-29257400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:29257000-29257400	Enhancers	Primary B cells from cord blood	blood
17	chr12:29257000-29257400	Enhancers	Primary T cells from cord blood	blood
18	chr12:29257000-29257600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:29257000-29257600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:29257000-29257600	Enhancers	Thymus	Thymus
21	chr12:29257000-29257800	Enhancers	GM12878-XiMat	blood
22	chr12:29257000-29258400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr12:29257000-29258400	Enhancers	Fetal Thymus	thymus
24	chr12:29257000-29258600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:29257000-29259800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:29257200-29257400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr12:29257200-29257800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:29257200-29258000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr12:29257200-29258400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:29257200-29258800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr12:29257200-29259000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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