Variant report

Variant	rs9940707
Chromosome Location	chr16:71800962-71800963
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71795022..71797414-chr16:71798658..71803314,4	MCF-7	breast:
2	chr16:71792577..71794560-chr16:71799391..71801593,2	MCF-7	breast:
3	chr16:71784075..71786608-chr16:71800561..71802768,2	MCF-7	breast:
4	chr16:71799645..71801237-chr16:71841138..71842836,2	MCF-7	breast:
5	chr16:71800568..71802232-chr16:71804201..71806010,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10083757	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10220961	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1035545	0.92[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap]
rs1058747	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap]
rs10775326	0.81[EUR][1000 genomes]
rs11075895	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11075900	0.93[ASN][1000 genomes]
rs11075902	0.87[ASN][1000 genomes]
rs11539980	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs11640725	0.82[ASN][1000 genomes]
rs11641873	0.89[ASN][1000 genomes]
rs11645467	0.90[ASN][1000 genomes]
rs11646635	0.90[ASN][1000 genomes]
rs11646748	0.90[ASN][1000 genomes]
rs11647873	0.82[EUR][1000 genomes]
rs11648240	0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]
rs11648674	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11859729	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11862798	0.82[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap]
rs11865683	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11866795	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12149092	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12149496	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12149873	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12444484	0.89[JPT][hapmap]
rs12447856	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12597065	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12598902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12920243	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12922859	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12923644	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12925587	0.85[ASN][1000 genomes]
rs12926987	0.82[ASN][1000 genomes]
rs12928187	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12930206	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12930418	0.83[EUR][1000 genomes]
rs12932850	0.94[GIH][hapmap];0.89[JPT][hapmap]
rs13380425	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1392483	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1392487	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs172650	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs2010428	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036337	0.90[ASN][1000 genomes]
rs2036338	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2270829	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270830	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2270831	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2270832	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2278031	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2303225	0.94[JPT][hapmap]
rs2335716	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2432520	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs28439683	0.82[ASN][1000 genomes]
rs28582831	0.80[ASN][1000 genomes]
rs28704189	0.84[ASN][1000 genomes]
rs34158217	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34161748	0.82[ASN][1000 genomes]
rs34734042	0.83[ASN][1000 genomes]
rs35173463	0.90[ASN][1000 genomes]
rs35939203	0.83[EUR][1000 genomes]
rs3751817	0.84[ASN][1000 genomes]
rs3752681	0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap]
rs3829537	0.82[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap]
rs3886515	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4444347	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4788442	0.90[ASN][1000 genomes]
rs4788549	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4788551	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4788552	0.84[ASN][1000 genomes]
rs4788554	0.93[ASN][1000 genomes]
rs4788558	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4788808	0.81[CHD][hapmap]
rs4788809	0.82[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap]
rs4788812	0.83[JPT][hapmap]
rs4788817	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs4788821	0.94[GIH][hapmap];0.88[JPT][hapmap]
rs4788826	0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4788827	0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs60881203	0.81[ASN][1000 genomes]
rs6499532	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6499539	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7185997	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7186859	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7187877	0.83[EUR][1000 genomes]
rs7188406	0.89[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs7191593	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7192956	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7195840	0.82[EUR][1000 genomes]
rs7196498	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7201228	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7201754	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7202288	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7203168	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7203216	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7203231	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7404381	0.94[ASN][1000 genomes]
rs7501228	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8048057	0.92[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs8048210	0.92[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs8051760	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8052489	0.81[ASN][1000 genomes]
rs8052999	0.89[ASN][1000 genomes]
rs8053070	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8056823	0.81[EUR][1000 genomes]
rs8060867	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs8061613	0.83[EUR][1000 genomes]
rs8061970	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8062441	0.92[ASN][1000 genomes]
rs8062477	0.92[ASN][1000 genomes]
rs8063535	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8203	0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap]
rs904763	0.91[CHD][hapmap]
rs918721	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs951453	0.90[ASN][1000 genomes]
rs951939	0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs979789	0.92[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9921270	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9922054	0.84[ASN][1000 genomes]
rs9925069	0.83[ASN][1000 genomes]
rs9925228	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9927336	0.80[ASN][1000 genomes]
rs9927437	0.81[ASN][1000 genomes]
rs9936903	0.82[ASN][1000 genomes]
rs9937280	0.82[ASN][1000 genomes]
rs9939455	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9940217	0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9940990	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]

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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv1817133	chr16:71705908-71837477	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
3	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	89 gene(s)	inside rSNPs	diseases
4	esv1819402	chr16:71755852-71816899	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
5	esv1815957	chr16:71790812-71816899	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9940707	PLEKHG4	cis	parietal	SCAN
rs9940707	PHLPP2	cis	cerebellum	SCAN
rs9940707	TMED6	cis	parietal	SCAN
rs9940707	SLC9A5	cis	cerebellum	SCAN
rs9940707	CHTF8	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71761000-71805600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:71762200-71811400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:71763200-71812600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr16:71763400-71802200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr16:71763600-71801400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr16:71763600-71812400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:71763800-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr16:71764000-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr16:71764000-71813000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr16:71764800-71802600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr16:71770800-71810600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr16:71770800-71813800	Strong transcription	Liver	Liver
13	chr16:71771000-71812200	Strong transcription	Placenta	Placenta
14	chr16:71779600-71841800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:71780000-71821400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr16:71783800-71820600	Weak transcription	Psoas Muscle	Psoas
17	chr16:71784000-71811200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:71785400-71808800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr16:71786400-71802200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr16:71786400-71805200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr16:71786600-71809800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr16:71787000-71802200	Strong transcription	Fetal Thymus	thymus
23	chr16:71788000-71806600	Weak transcription	Stomach Mucosa	stomach
24	chr16:71789800-71802200	Strong transcription	GM12878-XiMat	blood
25	chr16:71792600-71801000	Weak transcription	Fetal Brain Female	brain
26	chr16:71792600-71806600	Weak transcription	Fetal Brain Male	brain
27	chr16:71792800-71801600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:71792800-71803400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr16:71792800-71805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr16:71792800-71809600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr16:71792800-71811000	Weak transcription	Small Intestine	intestine
32	chr16:71793200-71808800	Strong transcription	Fetal Intestine Large	intestine
33	chr16:71793200-71830400	Weak transcription	Fetal Heart	heart
34	chr16:71794000-71808600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr16:71794600-71802200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr16:71794800-71802200	Strong transcription	Dnd41	blood
37	chr16:71795000-71802200	Strong transcription	Primary B cells from cord blood	blood
38	chr16:71796800-71802200	Strong transcription	HSMM	muscle
39	chr16:71796800-71804200	Weak transcription	Colon Smooth Muscle	Colon
40	chr16:71797000-71801400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr16:71797000-71803000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr16:71797000-71804400	Weak transcription	Left Ventricle	heart
43	chr16:71797000-71804400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr16:71797000-71807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr16:71797000-71807200	Weak transcription	Esophagus	oesophagus
46	chr16:71797000-71807200	Weak transcription	Gastric	stomach
47	chr16:71797000-71807200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr16:71797000-71807200	Weak transcription	NHLF	lung
49	chr16:71797000-71823600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:71797200-71801000	Weak transcription	Primary T cells from cord blood	blood

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