Variant report

Variant	rs3796870
Chromosome Location	chr4:15811532-15811533
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	chr4:15809317..15811696-chr4:15960415..15963386,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10004415	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10016073	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10016948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10939635	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1800051	0.82[CHD][hapmap]
rs2286552	0.82[CHD][hapmap]
rs2286553	0.82[CHD][hapmap]
rs28864507	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756243	0.82[CHD][hapmap]
rs3775952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775955	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796866	0.82[CHD][hapmap]
rs3796872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796873	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3796874	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796875	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796876	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3822256	0.85[CHB][hapmap]
rs3822257	0.81[CHB][hapmap]
rs4285083	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4481229	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4508877	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs4580644	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs55934802	0.87[ASN][1000 genomes]
rs55944292	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6449184	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449185	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6449186	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449187	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449188	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449189	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6449191	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6449192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449194	0.89[ASN][1000 genomes]
rs6449195	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs6449197	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs6449198	0.86[ASN][1000 genomes]
rs6449199	0.87[ASN][1000 genomes]
rs6449200	0.87[ASN][1000 genomes]
rs6819300	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6820962	0.82[ASN][1000 genomes]
rs6836374	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs6843266	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6844578	0.86[ASN][1000 genomes]
rs6852105	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6852728	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6853339	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6853351	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858514	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7659546	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7661891	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7663941	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7665303	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7665330	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7666953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7667590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7668511	0.81[EUR][1000 genomes]
rs7679308	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7688839	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690685	0.81[CHB][hapmap]
rs7690854	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9884223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9884920	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9990613	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv10460	chr4:15757611-15818206	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1013204	chr4:15762970-15836237	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1010597	chr4:15776181-15836237	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796870	SLAMF8	trans	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15794000-15812200	Genic enhancers	Dnd41	blood
2	chr4:15808000-15813200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:15808400-15819400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:15810200-15811600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr4:15810400-15811600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:15810400-15811800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr4:15810800-15821600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:15811000-15811800	Enhancers	Primary T cells from cord blood	blood
9	chr4:15811200-15811800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr4:15811200-15818600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:15811400-15811600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr4:15811400-15811600	Enhancers	Primary B cells from cord blood	blood
13	chr4:15811400-15811600	Weak transcription	Thymus	Thymus
14	chr4:15811400-15811800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:15811400-15813200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:15811400-15813400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:15811400-15813400	Weak transcription	Psoas Muscle	Psoas
18	chr4:15811400-15817800	Weak transcription	Fetal Thymus	thymus
19	chr4:15811400-15818600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:15811400-15818600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:15811400-15818800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:15811400-15819400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr4:15811400-15819800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:15811400-15820000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:15811400-15827000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:15811400-15851200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:15811400-15852200	Weak transcription	Spleen	Spleen

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