Variant report

Variant	rs12679345
Chromosome Location	chr8:95564533-95564534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr8:95564093-95564556	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:95564422..95566417-chr8:95730460..95733624,3	K562	blood:
2	chr8:95564422..95566417-chr8:95731300..95733624,2	K562	blood:
3	chr8:95564312..95566828-chr8:95731001..95732970,2	MCF-7	breast:
4	chr8:95563755..95566398-chr8:95651251..95655119,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253704	TF binding region
ENSG00000261437	Chromatin interaction
ENSG00000104413	Chromatin interaction
ENSG00000156162	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10104041	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10111287	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1023767	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]
rs1048029	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1055800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10956915	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10956919	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11986009	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11992893	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12540967	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12541408	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12543207	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12543730	0.94[ASN][1000 genomes]
rs12678305	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12680418	0.83[CHB][hapmap]
rs12680842	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12680855	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12680965	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12681564	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13258635	0.83[CHB][hapmap]
rs1470153	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16916874	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16916881	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1992370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2114212	0.83[CHB][hapmap]
rs2304764	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2381882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2381885	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28729295	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28817653	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4269508	0.93[EUR][1000 genomes]
rs4366055	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4373498	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4735300	0.83[CHB][hapmap]
rs55897841	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56042558	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56302978	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56716157	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60655325	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72674832	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72674843	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72674852	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72674855	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72674861	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72674866	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72674867	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72674877	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7829886	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs957447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs957448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
6	nsv1017256	chr8:95555083-95570079	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1026768	chr8:95556054-95569566	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1033318	chr8:95556054-95576338	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1032065	chr8:95556054-95578349	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1016339	chr8:95556054-95585807	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1021702	chr8:95556054-95589194	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1033345	chr8:95556375-95570533	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	9 gene(s)	inside rSNPs	diseases
13	nsv1029802	chr8:95556959-95578349	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	esv3584580	chr8:95557287-95576350	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv438072	chr8:95558694-95571443	Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv429929	chr8:95564533-95676894	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12679345	PLEKHF2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95543200-95564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr8:95543200-95564800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:95546200-95564800	Weak transcription	Esophagus	oesophagus
4	chr8:95547000-95565000	Weak transcription	Pancreas	Pancrea
5	chr8:95551600-95564800	Weak transcription	Thymus	Thymus
6	chr8:95552200-95565000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:95554400-95564800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr8:95554600-95565000	Weak transcription	Spleen	Spleen
9	chr8:95555000-95565000	Weak transcription	Lung	lung
10	chr8:95555200-95564600	Weak transcription	Fetal Kidney	kidney
11	chr8:95555600-95564800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr8:95558600-95564800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr8:95558600-95564800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr8:95559200-95564800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr8:95559200-95564800	Weak transcription	Placenta	Placenta
16	chr8:95561600-95565000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr8:95562000-95564600	Enhancers	Left Ventricle	heart
18	chr8:95562800-95564600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr8:95563000-95564600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr8:95563000-95564800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr8:95563200-95564600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr8:95563200-95564600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr8:95563200-95564600	Enhancers	Liver	Liver
24	chr8:95563200-95564600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr8:95563200-95564800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr8:95563200-95564800	Enhancers	Primary B cells from peripheral blood	blood
27	chr8:95563200-95564800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr8:95563200-95564800	Enhancers	Brain Substantia Nigra	brain
29	chr8:95563200-95565200	Flanking Active TSS	Dnd41	blood
30	chr8:95563400-95564800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr8:95563400-95564800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr8:95563400-95566800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr8:95563600-95564600	Enhancers	Primary T cells from cord blood	blood
34	chr8:95563600-95564600	Enhancers	Primary hematopoietic stem cells	blood
35	chr8:95563600-95564600	Enhancers	Brain Angular Gyrus	brain
36	chr8:95563600-95564600	Enhancers	Fetal Stomach	stomach
37	chr8:95563600-95564600	Enhancers	Rectal Smooth Muscle	rectum
38	chr8:95563600-95564800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr8:95563600-95565200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr8:95563800-95564600	Enhancers	Primary B cells from cord blood	blood
41	chr8:95563800-95564600	Enhancers	Adipose Nuclei	Adipose
42	chr8:95563800-95564600	Enhancers	Brain Hippocampus Middle	brain
43	chr8:95563800-95564600	Enhancers	Fetal Brain Female	brain
44	chr8:95563800-95564600	Enhancers	Ovary	ovary
45	chr8:95563800-95564600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr8:95563800-95564800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr8:95563800-95564800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr8:95563800-95564800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr8:95563800-95564800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr8:95563800-95564800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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