Variant report

Variant	rs2965753
Chromosome Location	chr16:69751385-69751386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69741680..69751385-chr16:69755023..69763559,18	MCF-7	breast:
2	chr16:69744834..69746849-chr16:69751166..69754416,4	MCF-7	breast:
3	chr16:69751147..69753338-chr16:69753585..69756622,3	K562	blood:
4	chr16:69743471..69745136-chr16:69748998..69751992,2	K562	blood:
5	chr16:69751147..69753902-chr16:69755122..69757880,2	K562	blood:
6	chr16:69749475..69752892-chr16:69758495..69762039,4	K562	blood:
7	chr16:69750532..69752121-chr16:69788605..69790298,2	MCF-7	breast:
8	chr16:69744485..69751443-chr16:69758986..69763141,9	MCF-7	breast:
9	chr16:69749611..69753867-chr16:69754025..69757950,6	MCF-7	breast:
10	chr16:69738931..69740863-chr16:69751048..69753277,2	K562	blood:
11	chr16:69746030..69749754-chr16:69749797..69753294,3	K562	blood:
12	chr16:69751124..69753690-chr16:69787246..69790211,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141101	Chromatin interaction
ENSG00000181019	Chromatin interaction
ENSG00000261602	Chromatin interaction
ENSG00000262136	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10517	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs10852459	0.82[CHB][hapmap]
rs11862697	1.00[CEU][hapmap]
rs12019048	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs1318651	1.00[CEU][hapmap]
rs13329844	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs16958997	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs16959059	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16959266	1.00[CEU][hapmap]
rs2088747	1.00[CEU][hapmap]
rs2291960	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs2304526	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2917667	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2917669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs2917681	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs2917682	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2917683	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2937125	0.82[CHB][hapmap]
rs2937126	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap]
rs2965757	0.86[CHB][hapmap]
rs2965759	1.00[CEU][hapmap]
rs3785075	0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs3790084	0.87[CEU][hapmap]
rs3790087	1.00[CEU][hapmap]
rs3790088	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs3826153	0.86[CHB][hapmap];0.92[CHD][hapmap]
rs3826154	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4247109	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs4442796	0.88[CEU][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4985527	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs4985547	0.82[CHB][hapmap]
rs6499249	0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs6499259	1.00[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs689452	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7359387	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs8057938	1.00[CEU][hapmap]
rs9888980	1.00[CEU][hapmap]
rs9888981	1.00[CEU][hapmap]
rs9888993	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs9889219	0.81[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap]
rs9921652	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs9922223	1.00[CEU][hapmap]
rs9924271	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs9924953	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9925037	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs9932486	1.00[CEU][hapmap]
rs9934681	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9936464	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9937018	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9938717	0.91[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs9940008	1.00[CEU][hapmap]

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	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	54 gene(s)	inside rSNPs	diseases
2	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv517207	chr16:69745145-69771914	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv103566	chr16:69751377-69751392	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2965753	PDP2	cis	parietal	SCAN
rs2965753	FUK	cis	parietal	SCAN
rs2965753	GFOD2	cis	parietal	SCAN
rs2965753	NQO1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:69726000-69755800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:69726600-69759800	Weak transcription	Psoas Muscle	Psoas
4	chr16:69728200-69758600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr16:69728400-69759200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:69728600-69752000	Weak transcription	Fetal Brain Male	brain
7	chr16:69729400-69760000	Weak transcription	Brain Germinal Matrix	brain
8	chr16:69729400-69760000	Weak transcription	Ovary	ovary
9	chr16:69730000-69759000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr16:69730600-69759800	Weak transcription	Fetal Brain Female	brain
11	chr16:69730800-69759800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr16:69731800-69759600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr16:69731800-69759800	Weak transcription	Primary B cells from cord blood	blood
14	chr16:69731800-69759800	Weak transcription	Right Ventricle	heart
15	chr16:69733800-69759800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr16:69736000-69758600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr16:69737200-69758800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr16:69737400-69752600	Strong transcription	HSMMtube	muscle
19	chr16:69738800-69759800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr16:69739200-69759800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr16:69740800-69758800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr16:69741000-69759200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:69741000-69759400	Weak transcription	Small Intestine	intestine
24	chr16:69741400-69756600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr16:69741600-69753400	Strong transcription	HUVEC	blood vessel
26	chr16:69741600-69759800	Weak transcription	Primary T cells from cord blood	blood
27	chr16:69743800-69755600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr16:69743800-69758800	Weak transcription	Dnd41	blood
29	chr16:69743800-69760000	Weak transcription	Fetal Kidney	kidney
30	chr16:69744000-69759800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr16:69744800-69752800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr16:69745000-69752400	Strong transcription	Fetal Intestine Small	intestine
33	chr16:69745000-69752600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr16:69745000-69752600	Strong transcription	Fetal Stomach	stomach
35	chr16:69745000-69752600	Strong transcription	Lung	lung
36	chr16:69745000-69752800	Strong transcription	Hela-S3	cervix
37	chr16:69745400-69755400	Weak transcription	K562	blood
38	chr16:69745400-69759800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr16:69745600-69757800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:69745800-69752600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr16:69745800-69758400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr16:69746000-69752800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr16:69746000-69752800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr16:69746400-69756800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr16:69746600-69752600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr16:69746600-69755800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr16:69746600-69758800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr16:69746800-69754200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr16:69746800-69755800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr16:69747000-69759000	Weak transcription	H1 Cell Line	embryonic stem cell

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