Variant report

Variant	rs28706886
Chromosome Location	chr7:7609740-7609741
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	CUX1	chr7:7609507-7609780	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:7606180-7609855	GM12892	blood:	n/a	n/a
3	POLR2A	chr7:7609690-7609760	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr7:7607548-7610838	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:7607549-7609826	GM12892	blood:	n/a	n/a
6	BRCA1	chr7:7609643-7609862	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:7606226-7609771	GM12892	blood:	n/a	n/a
8	POLR2A	chr7:7606063-7609760	GM19099	blood:	n/a	n/a
9	POLR2A	chr7:7608142-7609744	GM12892	blood:	n/a	n/a
10	POU2F2	chr7:7608598-7609751	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:7606056-7610648	GM12891	blood:	n/a	n/a
12	NFATC1	chr7:7608506-7610011	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:7606087-7610683	GM12892	blood:	n/a	n/a
14	BHLHE40	chr7:7609547-7609830	GM12878	blood:	n/a	n/a
15	POLR2A	chr7:7607888-7609742	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:7606006-7610933	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:7606174-7610054	GM18505	blood:	n/a	n/a
18	POLR2A	chr7:7606127-7610748	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:7606253-7610047	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7605291..7607922-chr7:7608027..7610593,4	MCF-7	breast:
2	chr7:7588099..7594648-chr7:7604621..7611487,9	MCF-7	breast:
3	chr7:7608142..7610362-chr7:7619716..7621780,2	K562	blood:

Variant related genes	Relation type
ENSG00000272894	TF binding region
ENSG00000272732	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000272894	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10224056	1.00[EUR][1000 genomes]
rs10244757	1.00[EUR][1000 genomes]
rs10246969	1.00[EUR][1000 genomes]
rs10254036	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10257279	1.00[EUR][1000 genomes]
rs10273001	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13438746	1.00[EUR][1000 genomes]
rs17168622	1.00[EUR][1000 genomes]
rs2348340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28422034	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28488380	1.00[EUR][1000 genomes]
rs28564742	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28602361	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56845168	1.00[EUR][1000 genomes]
rs57830645	1.00[EUR][1000 genomes]
rs60663837	1.00[EUR][1000 genomes]
rs61285017	1.00[EUR][1000 genomes]
rs73349819	1.00[EUR][1000 genomes]
rs73349821	1.00[EUR][1000 genomes]
rs73349832	1.00[EUR][1000 genomes]
rs73353651	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers 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 miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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 miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS 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	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers 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	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7606200-7609800	Active TSS	GM12878-XiMat	blood
2	chr7:7607200-7609800	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr7:7607200-7648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:7607400-7610200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:7607400-7612400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
6	chr7:7607400-7646400	Weak transcription	Esophagus	oesophagus
7	chr7:7607400-7648200	Weak transcription	Lung	lung
8	chr7:7607600-7610600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:7607600-7610600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr7:7607600-7612000	Weak transcription	Ovary	ovary
11	chr7:7607600-7612200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:7607600-7613400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:7607600-7646400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:7607600-7648400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:7607800-7621400	Weak transcription	Aorta	Aorta
16	chr7:7608000-7610600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr7:7608000-7612800	Weak transcription	HSMMtube	muscle
18	chr7:7608200-7612200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:7608200-7612400	Weak transcription	Fetal Intestine Large	intestine
20	chr7:7608200-7648800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:7608400-7609800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:7608400-7609800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr7:7608400-7610200	Weak transcription	Pancreas	Pancrea
24	chr7:7608400-7611600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:7608400-7630800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:7608400-7648600	Weak transcription	NH-A	brain
27	chr7:7608600-7609800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:7608600-7610400	Enhancers	Brain Hippocampus Middle	brain
29	chr7:7608600-7610800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr7:7608600-7611000	Weak transcription	NHLF	lung
31	chr7:7608600-7612200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr7:7608600-7612200	Weak transcription	HMEC	breast
33	chr7:7608600-7612400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:7608800-7609800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr7:7608800-7609800	Enhancers	Brain Germinal Matrix	brain
36	chr7:7608800-7610400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr7:7608800-7620600	Weak transcription	Fetal Stomach	stomach
38	chr7:7608800-7621200	Weak transcription	Fetal Intestine Small	intestine
39	chr7:7608800-7622200	Weak transcription	HUVEC	blood vessel
40	chr7:7608800-7635800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:7609000-7609800	Weak transcription	Brain Angular Gyrus	brain
42	chr7:7609000-7611200	Weak transcription	Fetal Lung	lung
43	chr7:7609000-7611400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:7609000-7612000	Weak transcription	Placenta	Placenta
45	chr7:7609000-7612200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:7609000-7612400	Weak transcription	Fetal Brain Female	brain
47	chr7:7609000-7621000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr7:7609000-7621200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr7:7609200-7609800	Enhancers	Primary hematopoietic stem cells	blood
50	chr7:7609200-7610000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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