Variant report

Variant	rs1023767
Chromosome Location	chr8:95530969-95530970
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	chr8:95523173..95526171-chr8:95528609..95531520,2	K562	blood:
2	chr8:95520876..95523333-chr8:95528954..95531055,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164944	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10104041	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10111287	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048029	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1055800	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10956915	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10956919	0.96[ASN][1000 genomes]
rs11986009	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11992893	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12540967	0.96[ASN][1000 genomes]
rs12541408	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs12543207	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12543730	0.96[ASN][1000 genomes]
rs12678305	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12679345	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12680842	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs12680855	0.95[ASN][1000 genomes]
rs12680965	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12681564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1470153	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16916874	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16916881	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992370	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304764	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2381882	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2381885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28729295	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28817653	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4269508	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4366055	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4373498	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4735297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs55897841	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56042558	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56302978	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56716157	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60655325	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72674832	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72674843	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72674852	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72674855	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72674861	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72674866	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72674867	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72674877	0.96[ASN][1000 genomes]
rs7829886	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs957447	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs957448	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv611750	chr8:95519205-95574634	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1023767	PLEKHF2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95493000-95549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:95495200-95538400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr8:95495600-95541000	Weak transcription	Esophagus	oesophagus
4	chr8:95497200-95564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr8:95498400-95554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:95499400-95533400	Strong transcription	Placenta	Placenta
7	chr8:95499400-95552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr8:95501200-95541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:95515600-95534200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr8:95516200-95534000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:95516800-95554600	Strong transcription	Fetal Thymus	thymus
12	chr8:95517600-95538600	Weak transcription	Fetal Brain Male	brain
13	chr8:95517600-95540200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr8:95518000-95534000	Weak transcription	Psoas Muscle	Psoas
15	chr8:95518800-95534000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr8:95520400-95532200	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr8:95520400-95532400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr8:95520400-95532800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr8:95520400-95532800	Strong transcription	Fetal Intestine Large	intestine
20	chr8:95520400-95534600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr8:95520400-95534800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr8:95520400-95534800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr8:95520400-95535000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:95520400-95535000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr8:95520400-95555200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr8:95520600-95532200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr8:95520600-95534400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr8:95520600-95534600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:95520600-95536000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr8:95520600-95552400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr8:95520800-95532200	Strong transcription	Dnd41	blood
32	chr8:95521000-95532000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr8:95521000-95533600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr8:95522600-95533000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr8:95523000-95532400	Strong transcription	Liver	Liver
36	chr8:95523800-95536800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr8:95523800-95539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr8:95524000-95534000	Weak transcription	NHEK	skin
39	chr8:95524000-95538200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr8:95524000-95540400	Weak transcription	Colonic Mucosa	Colon
41	chr8:95524400-95531200	Weak transcription	HSMMtube	muscle
42	chr8:95525200-95538200	Weak transcription	Brain Substantia Nigra	brain
43	chr8:95525400-95532400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr8:95525600-95534600	Weak transcription	Brain Hippocampus Middle	brain
45	chr8:95526200-95532000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr8:95526600-95533600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr8:95527200-95534800	Strong transcription	Thymus	Thymus
48	chr8:95527400-95532800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr8:95527600-95548600	Strong transcription	Fetal Muscle Leg	muscle
50	chr8:95528000-95531000	Strong transcription	Fetal Brain Female	brain

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