Variant report

Variant	rs1646290
Chromosome Location	chr16:58789711-58789712
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	chr16:58715146..58717917-chr16:58788280..58790471,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11076263	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11076270	0.82[EUR][1000 genomes]
rs11643969	0.83[EUR][1000 genomes]
rs11646756	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12325054	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12325510	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596434	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12598527	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12599931	0.82[EUR][1000 genomes]
rs12600201	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12600206	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12709013	0.82[EUR][1000 genomes]
rs12926993	0.82[EUR][1000 genomes]
rs12927495	0.83[EUR][1000 genomes]
rs12928733	0.94[EUR][1000 genomes]
rs12930298	0.80[EUR][1000 genomes]
rs12935488	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1364346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473205	0.83[EUR][1000 genomes]
rs1473206	0.83[EUR][1000 genomes]
rs151817	0.84[EUR][1000 genomes]
rs1615326	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616798	0.89[EUR][1000 genomes]
rs1627257	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1628029	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1646262	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1646270	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646273	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1646276	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1646277	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646283	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646289	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657162	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1657165	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1657168	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1657175	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657179	0.82[EUR][1000 genomes]
rs173992	0.81[ASN][1000 genomes]
rs244919	0.84[EUR][1000 genomes]
rs257623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs257625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs257626	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30843	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36098613	0.94[EUR][1000 genomes]
rs62064940	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62066381	0.95[EUR][1000 genomes]
rs62066382	0.89[EUR][1000 genomes]
rs62066815	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066843	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7185513	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8046667	0.82[EUR][1000 genomes]
rs8049572	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8054482	0.81[EUR][1000 genomes]
rs982848	0.84[EUR][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	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
4	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58776600-58790000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:58784200-58790200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:58788600-58789800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr16:58789200-58790000	Enhancers	H9 Cell Line	embryonic stem cell
5	chr16:58789400-58789800	Enhancers	Dnd41	blood
6	chr16:58789400-58790000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr16:58789600-58789800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr16:58789600-58789800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr16:58789600-58789800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr16:58789600-58789800	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr16:58789600-58790000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr16:58789600-58790000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr16:58789600-58790000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr16:58789600-58790000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr16:58789600-58790000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr16:58789600-58790000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr16:58789600-58790000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr16:58789600-58790000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr16:58789600-58790000	Enhancers	HUVEC	blood vessel
20	chr16:58789600-58790400	Enhancers	Primary T cells from cord blood	blood
21	chr16:58789600-58790400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr16:58789600-58790600	Enhancers	Primary hematopoietic stem cells	blood
23	chr16:58789600-58790600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr16:58789600-58791000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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