Variant report

Variant	rs2301936
Chromosome Location	chr7:7679107-7679108
allele	A/C
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	POLR2A	chr7:7679078-7681429	HepG2	liver:	n/a	n/a
2	SMARCC1	chr7:7679092-7681404	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:7678812-7681214	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr7:7679081-7680950	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr7:7679060-7681323	GM12891	blood:	n/a	n/a
6	MXI1	chr7:7678754-7682381	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr7:7678993-7681329	GM12892	blood:	n/a	n/a
8	POLR2A	chr7:7679078-7681236	GM19099	blood:	n/a	n/a
9	MTA3	chr7:7678970-7681157	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:7679106-7679243	K562	blood:	n/a	n/a
11	POLR2A	chr7:7679068-7681273	GM12878	blood:	n/a	n/a
12	SIN3A	chr7:7679037-7681506	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr7:7679048-7679343	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr7:7678988-7681348	GM12878	blood:	n/a	n/a
15	POLR2A	chr7:7679034-7681483	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr7:7679007-7681545	K562	blood:	n/a	n/a
17	POLR2A	chr7:7679088-7681837	PBDE	blood:	n/a	n/a
18	MXI1	chr7:7679099-7679134	K562	blood:	n/a	n/a
19	POLR2A	chr7:7679043-7681348	GM18505	blood:	n/a	n/a
20	POLR2A	chr7:7678588-7681417	K562	blood:	n/a	n/a
21	POLR2A	chr7:7679051-7679357	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr7:7679036-7681599	GM12878	blood:	n/a	n/a
23	MXI1	chr7:7679055-7681265	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:7678973-7681034	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr7:7679051-7680189	GM12891	blood:	n/a	n/a
26	E2F4	chr7:7678977-7681255	MCF10A-Er-Src	breast:	n/a	chr7:7679772-7679783 chr7:7679769-7679786 chr7:7679776-7679783 chr7:7679769-7679786 chr7:7680071-7680082 chr7:7680622-7680631
27	POLR2A	chr7:7679100-7681361	GM12878	blood:	n/a	n/a
28	PML	chr7:7679078-7681200	GM12878	blood:	n/a	n/a
29	RFX5	chr7:7677457-7682740	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7602591..7604094-chr7:7678775..7680350,2	K562	blood:
2	chr7:7603046..7608569-chr7:7677123..7682101,8	MCF-7	breast:
3	chr7:7679018..7681584-chr7:8008760..8011156,4	K562	blood:
4	chr7:7673907..7678610-chr7:7678691..7681851,6	MCF-7	breast:
5	chr7:7605040..7608458-chr7:7677009..7681661,8	K562	blood:
6	chr7:7605830..7608267-chr7:7679102..7681869,5	MCF-7	breast:
7	chr7:7672448..7678421-chr7:7678475..7681557,8	K562	blood:
8	chr7:7678479..7681346-chr7:8300009..8302111,2	K562	blood:
9	chr7:7658111..7660487-chr7:7677718..7679427,3	K562	blood:

Variant related genes	Relation type
RPA3	TF binding region
RPA3-AS1	TF binding region
ENSG00000244239	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000272745	Chromatin interaction
ENSG00000003147	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000233108	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000229970	Chromatin interaction
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs28916321	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3735460	0.80[EUR][1000 genomes]
rs6463710	0.90[TSI][hapmap]

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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv1034199	chr7:7617835-7691176	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv606044	chr7:7652372-7727101	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2301936	RPA3	cis	lesional skin	skin_eQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7671400-7679200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:7671600-7679200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:7671600-7679200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr7:7672000-7679200	Weak transcription	Aorta	Aorta
5	chr7:7672200-7679200	Weak transcription	Gastric	stomach
6	chr7:7672400-7679200	Weak transcription	Brain Substantia Nigra	brain
7	chr7:7672600-7679200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:7672600-7679200	Weak transcription	Ovary	ovary
9	chr7:7672600-7679400	Weak transcription	Right Ventricle	heart
10	chr7:7672800-7679200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:7674000-7679200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr7:7674000-7679400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:7674200-7679200	Weak transcription	Placenta	Placenta
14	chr7:7674600-7679200	Weak transcription	Colonic Mucosa	Colon
15	chr7:7675000-7679200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:7675000-7679200	Weak transcription	Pancreas	Pancrea
17	chr7:7675600-7679200	Weak transcription	Small Intestine	intestine
18	chr7:7676200-7679200	Weak transcription	Esophagus	oesophagus
19	chr7:7676200-7679200	Weak transcription	Left Ventricle	heart
20	chr7:7676200-7679200	Weak transcription	Lung	lung
21	chr7:7677600-7679200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:7677600-7679200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:7678600-7679600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr7:7678600-7681200	Active TSS	HMEC	breast
25	chr7:7678800-7679200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:7678800-7679200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:7678800-7679200	Flanking Active TSS	NHDF-Ad	bronchial
28	chr7:7678800-7679400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr7:7678800-7679400	Flanking Active TSS	Dnd41	blood
30	chr7:7678800-7679600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:7678800-7679600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:7678800-7679600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:7678800-7679600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:7678800-7679600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:7678800-7681200	Active TSS	A549	lung
36	chr7:7678800-7681400	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr7:7678800-7681400	Active TSS	K562	blood
38	chr7:7678800-7681600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:7679000-7679200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:7679000-7679200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:7679000-7679200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr7:7679000-7679200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr7:7679000-7679200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:7679000-7679200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr7:7679000-7679200	Enhancers	Primary B cells from peripheral blood	blood
46	chr7:7679000-7679200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr7:7679000-7679200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr7:7679000-7679200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:7679000-7679200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:7679000-7679200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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