Variant report

Variant	rs17307409
Chromosome Location	chr16:70752139-70752140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70751340..70753059-chr16:70768605..70771567,2	MCF-7	breast:
2	chr16:70740784..70746452-chr16:70747278..70752169,9	K562	blood:
3	chr16:70748104..70753433-chr16:70779056..70781695,7	MCF-7	breast:
4	chr16:70747879..70752178-chr16:70754716..70759017,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260156	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10153136	0.88[CHB][hapmap]
rs2290614	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2902830	1.00[JPT][hapmap]
rs3743988	1.00[JPT][hapmap]
rs3785425	0.88[CHB][hapmap]
rs4985423	1.00[JPT][hapmap]
rs57682106	0.94[ASN][1000 genomes]
rs6499335	1.00[JPT][hapmap]
rs7190561	1.00[JPT][hapmap]
rs7203578	1.00[JPT][hapmap]
rs9673512	1.00[CHB][hapmap]
rs9939763	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906876	chr16:70677785-70757555	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv906877	chr16:70677785-70766378	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
6	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	19 gene(s)	inside rSNPs	diseases
7	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS 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	19 gene(s)	inside rSNPs	diseases
8	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1059226	chr16:70708698-70779144	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv906889	chr16:70724001-70790831	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv906890	chr16:70740707-70790831	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17307409	TPPP3	cis	parietal	SCAN
rs17307409	CENPT	cis	parietal	SCAN
rs17307409	ELAVL2	trans	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70720400-70753200	Weak transcription	Primary B cells from cord blood	blood
2	chr16:70727000-70770800	Weak transcription	GM12878-XiMat	blood
3	chr16:70731400-70755000	Weak transcription	Small Intestine	intestine
4	chr16:70733200-70759400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr16:70733400-70754000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:70733800-70753400	Weak transcription	Dnd41	blood
7	chr16:70737000-70753800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr16:70741000-70752800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr16:70741400-70753400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr16:70742400-70752600	Weak transcription	Hela-S3	cervix
11	chr16:70744000-70754800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr16:70744200-70752600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr16:70744400-70752600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr16:70744400-70752600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr16:70744400-70753000	Enhancers	Fetal Muscle Leg	muscle
16	chr16:70744400-70754000	Weak transcription	Aorta	Aorta
17	chr16:70745200-70753600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr16:70745400-70753200	Enhancers	Placenta	Placenta
19	chr16:70746800-70753200	Weak transcription	Primary T cells from cord blood	blood
20	chr16:70747400-70753400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr16:70749400-70752600	Weak transcription	Brain Substantia Nigra	brain
22	chr16:70749400-70753800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:70749600-70754200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr16:70749800-70752600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr16:70749800-70752800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr16:70749800-70754200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr16:70749800-70759000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:70749800-70759600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr16:70750000-70752600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr16:70750000-70752600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr16:70750000-70752800	Enhancers	Fetal Muscle Trunk	muscle
32	chr16:70750000-70753400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr16:70750000-70753600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr16:70750000-70753800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr16:70750200-70752600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr16:70750200-70752600	Weak transcription	Thymus	Thymus
37	chr16:70750200-70752800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr16:70750200-70753000	Enhancers	Fetal Lung	lung
39	chr16:70750200-70753600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr16:70750200-70753600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:70750200-70753800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr16:70750200-70759000	Weak transcription	Esophagus	oesophagus
43	chr16:70750200-70759600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr16:70750400-70752400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr16:70750400-70752400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr16:70750400-70752800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr16:70750400-70752800	Enhancers	Brain Germinal Matrix	brain
48	chr16:70750400-70753400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr16:70750400-70753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr16:70750400-70753600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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