Variant report

Variant	rs3909598
Chromosome Location	chr4:143506298-143506299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143504828..143506931-chr4:143519506..143521581,2	MCF-7	breast:
2	chr4:143506127..143509971-chr4:143766689..143769613,3	MCF-7	breast:
3	chr4:143500805..143505474-chr4:143506198..143510194,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10002299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10002937	0.83[AFR][1000 genomes]
rs10008407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10008556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10008852	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10010772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10013934	0.89[AFR][1000 genomes]
rs10014555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10014747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10014849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10014859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10017037	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10019887	0.89[AFR][1000 genomes]
rs10020192	0.83[AFR][1000 genomes]
rs10021085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10032060	0.83[AFR][1000 genomes]
rs12331694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12331834	0.83[AFR][1000 genomes]
rs1425529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1425530	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17016384	1.00[AMR][1000 genomes]
rs17016395	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17016424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17016428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17016465	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17016469	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17016476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2113995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2162106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2162107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28413753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28481559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28562975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28612359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28620580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28647363	1.00[ASN][1000 genomes]
rs28693572	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28701753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28713525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28753390	0.83[AFR][1000 genomes]
rs28758948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28846169	1.00[ASN][1000 genomes]
rs3909597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4340863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4361463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4560493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4560494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4563566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4579200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56258617	1.00[ASN][1000 genomes]
rs61289420	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461660	chr4:143437219-143538179	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv595605	chr4:143437219-143538179	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143489800-143519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:143490800-143519200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:143493600-143510800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:143501400-143511000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:143503800-143512400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:143503800-143514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:143504000-143508600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:143504000-143511400	Weak transcription	Primary T cells from cord blood	blood
9	chr4:143504600-143508200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:143505400-143508600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:143505600-143506800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:143505600-143507400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:143505600-143507600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr4:143506200-143506400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:143506200-143507000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:143506200-143507400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:143506200-143507600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:143506200-143508800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:143506200-143510200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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