Variant report

Variant	rs9934459
Chromosome Location	chr16:48369127-48369128
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	chr16:48367808..48369426-chr16:48417936..48419640,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196470	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12102896	1.00[AFR][1000 genomes]
rs13332870	1.00[AMR][1000 genomes]
rs13335175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336203	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13337923	1.00[AMR][1000 genomes]
rs28361908	1.00[AMR][1000 genomes]
rs28379458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28473019	1.00[AMR][1000 genomes]
rs28539217	1.00[AMR][1000 genomes]
rs28599555	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28661941	1.00[AMR][1000 genomes]
rs28848294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9922477	1.00[AMR][1000 genomes]
rs9926437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926749	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs9927124	1.00[AMR][1000 genomes]
rs9928527	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9929780	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9931267	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9931866	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9932677	1.00[AMR][1000 genomes]
rs9933958	1.00[AMR][1000 genomes]
rs9934175	1.00[ASW][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934918	1.00[AMR][1000 genomes]
rs9936494	1.00[AMR][1000 genomes]
rs9936636	1.00[AMR][1000 genomes]
rs9936892	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs9938115	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9938350	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9938594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9940237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9941354	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv1821072	chr16:48268318-48504364	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv833219	chr16:48290595-48459301	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1061708	chr16:48304343-48482594	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv542917	chr16:48304343-48482594	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv2758424	chr16:48329437-48479754	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv2758645	chr16:48329437-48479754	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48338600-48381200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:48343400-48375600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:48347600-48384800	Weak transcription	Fetal Kidney	kidney
4	chr16:48352000-48369600	Weak transcription	HSMM	muscle
5	chr16:48352200-48395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:48355800-48375800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:48355800-48384800	Weak transcription	Small Intestine	intestine
8	chr16:48363400-48383400	Weak transcription	HUVEC	blood vessel
9	chr16:48364400-48378800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:48365000-48381400	Weak transcription	Pancreas	Pancrea
11	chr16:48365000-48388200	Weak transcription	Right Atrium	heart
12	chr16:48365200-48378600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr16:48365200-48392400	Strong transcription	Liver	Liver
14	chr16:48365800-48377600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr16:48366200-48371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr16:48366400-48369600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr16:48366400-48377400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr16:48366600-48372600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr16:48366800-48377400	Strong transcription	Dnd41	blood
20	chr16:48367000-48370400	Strong transcription	Brain Angular Gyrus	brain
21	chr16:48367000-48378600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr16:48367000-48387000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr16:48367200-48370400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr16:48367200-48372600	Strong transcription	Fetal Muscle Leg	muscle
25	chr16:48367200-48387000	Strong transcription	Primary T cells from cord blood	blood
26	chr16:48367400-48372400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr16:48367400-48372400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr16:48367400-48378600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr16:48367400-48387000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr16:48367600-48369200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr16:48367600-48369400	Strong transcription	Brain Germinal Matrix	brain
32	chr16:48367600-48369400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr16:48367600-48369600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr16:48367600-48370000	Strong transcription	GM12878-XiMat	blood
35	chr16:48367600-48370400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr16:48367600-48377000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr16:48367600-48377400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr16:48367600-48378200	Strong transcription	Primary B cells from cord blood	blood
39	chr16:48367600-48378600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr16:48367600-48378800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr16:48367800-48369200	Strong transcription	Osteobl	bone
42	chr16:48367800-48369600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr16:48367800-48369800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr16:48367800-48369800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr16:48367800-48369800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr16:48367800-48370000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr16:48367800-48370400	Strong transcription	Brain Anterior Caudate	brain
48	chr16:48367800-48370400	Strong transcription	Fetal Lung	lung
49	chr16:48367800-48372800	Strong transcription	Primary hematopoietic stem cells	blood
50	chr16:48367800-48373400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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