Variant report

Variant	rs2057880
Chromosome Location	chr7:80549933-80549934
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	MAX	chr7:80549101-80550108	MCF-7	breast:	n/a	n/a
2	MAX	chr7:80547612-80550153	A549	lung:	n/a	chr7:80548020-80548027
3	RAD21	chr7:80549183-80550072	MCF-7	breast:	n/a	chr7:80549631-80549650
4	REST	chr7:80547725-80550010	A549	lung:	n/a	n/a
5	RAD21	chr7:80549266-80550026	HCT-116	colon:	n/a	chr7:80549631-80549650
6	TCF12	chr7:80547779-80550056	A549	lung:	n/a	chr7:80549858-80549867 chr7:80549951-80549959
7	SIX5	chr7:80549077-80550089	A549	lung:	n/a	n/a
8	CTCF	chr7:80549045-80550052	SK-N-SH	brain:	n/a	chr7:80549632-80549653 chr7:80549630-80549648
9	RAD21	chr7:80549329-80549960	A549	lung:	n/a	chr7:80549631-80549650
10	POLR2A	chr7:80547193-80551247	PANC-1	pancreas:	n/a	n/a
11	SMC3	chr7:80549058-80550240	SK-N-SH	brain:	n/a	chr7:80549632-80549646
12	FOSL2	chr7:80549070-80549969	A549	lung:	n/a	chr7:80549254-80549266
13	POLR2A	chr7:80542371-80551951	MCF-7	breast:	n/a	n/a
14	POLR2A	chr7:80547276-80550113	PANC-1	pancreas:	n/a	n/a
15	RAD21	chr7:80549331-80549983	HCT-116	colon:	n/a	chr7:80549631-80549650
16	RAD21	chr7:80547381-80551152	SK-N-SH	brain:	n/a	chr7:80548620-80548634 chr7:80549631-80549650
17	RAD21	chr7:80549330-80549984	A549	lung:	n/a	chr7:80549631-80549650
18	RAD21	chr7:80549328-80549975	MCF-7	breast:	n/a	chr7:80549631-80549650
19	SIN3AK20	chr7:80547324-80551268	MCF-7	breast:	n/a	n/a
20	CTCF	chr7:80547597-80550795	A549	lung:	n/a	chr7:80549632-80549653 chr7:80549630-80549648 chr7:80547725-80547732 chr7:80548621-80548634
21	MAX	chr7:80549429-80549995	A549	lung:	n/a	n/a
22	BCL3	chr7:80549359-80549998	A549	lung:	n/a	n/a
23	FOXA1	chr7:80549403-80549972	T-47D	breast:	n/a	n/a
24	CTCF	chr7:80549215-80549938	HCT-116	colon:	n/a	chr7:80549632-80549653 chr7:80549630-80549648

No.	Distal block	Cell Line	Cell type
1	chr7:80506016..80506631-chr7:80549904..80550579,2	MCF-7	breast:
2	chr19:41944180..41946970-chr7:80547778..80549990,2	MCF-7	breast:
3	chr7:80548775..80550728-chr7:80725629..80727229,2	MCF-7	breast:
4	chr7:80446232..80448105-chr7:80546951..80549936,2	MCF-7	breast:
5	chr7:80453386..80455160-chr7:80549437..80551338,2	MCF-7	breast:
6	chr7:80548784..80550699-chr7:80652671..80654608,2	MCF-7	breast:
7	chr7:80548724..80552228-chr7:81092186..81095551,3	MCF-7	breast:
8	chr7:80549184..80550786-chr7:80865135..80867870,2	MCF-7	breast:
9	chr5:90677371..90680085-chr7:80548730..80550389,2	MCF-7	breast:
10	chr7:80546356..80552735-chr7:80798673..80805379,14	MCF-7	breast:
11	chr7:80546517..80551479-chr7:80801945..80805775,5	MCF-7	breast:
12	chr7:80548873..80550374-chr7:80829934..80832081,2	MCF-7	breast:
13	chr6:27837988..27840286-chr7:80547684..80550334,2	MCF-7	breast:
14	chr7:80547567..80550681-chr7:81058746..81062625,3	MCF-7	breast:
15	chr17:65030555..65033441-chr7:80548839..80551076,2	MCF-7	breast:
16	chr7:80546955..80550718-chr7:80817331..80823169,5	MCF-7	breast:
17	chr7:80549638..80551457-chr7:81096415..81098240,2	MCF-7	breast:
18	chr7:80548728..80550741-chr7:80899992..80902009,2	MCF-7	breast:
19	chr1:149857039..149859334-chr7:80548386..80551320,2	MCF-7	breast:
20	chr7:80549186..80551426-chr7:81023686..81025197,2	MCF-7	breast:
21	chr7:80549472..80551455-chr7:80599232..80601743,2	MCF-7	breast:
22	chr7:80549150..80551514-chr7:80899704..80901338,2	MCF-7	breast:

Variant related genes	Relation type
SEMA3C	TF binding region
ENSG00000184260	Chromatin interaction
ENSG00000232968	Chromatin interaction
ENSG00000075223	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000224134	Chromatin interaction
ENSG00000226671	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000182572	Chromatin interaction
ENSG00000237896	Chromatin interaction
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3762017	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964151	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888524	chr7:80107798-80723062	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1028776	chr7:80414636-80555284	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1034690	chr7:80520004-80987682	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80548400-80552600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:80548400-80570000	Weak transcription	Gastric	stomach
3	chr7:80548800-80550400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:80548800-80550600	Weak transcription	Small Intestine	intestine
5	chr7:80548800-80552600	Weak transcription	Fetal Heart	heart
6	chr7:80549000-80550400	Weak transcription	Fetal Lung	lung
7	chr7:80549200-80550600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:80549200-80551000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:80549200-80551000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:80549200-80551400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:80549200-80552400	Weak transcription	Fetal Muscle Leg	muscle
12	chr7:80549200-80565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:80549400-80550000	Bivalent Enhancer	HepG2	liver
14	chr7:80549400-80550600	Flanking Active TSS	A549	lung
15	chr7:80549400-80550600	Weak transcription	Hela-S3	cervix
16	chr7:80549400-80550800	Weak transcription	Osteobl	bone
17	chr7:80549400-80551000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:80549400-80552400	Weak transcription	Fetal Kidney	kidney
19	chr7:80549400-80552600	Weak transcription	Psoas Muscle	Psoas
20	chr7:80549400-80553600	Weak transcription	Colonic Mucosa	Colon
21	chr7:80549400-80554400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr7:80549600-80550000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:80549600-80550000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:80549600-80550600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:80549600-80550600	Weak transcription	NH-A	brain
26	chr7:80549600-80550600	Enhancers	NHEK	skin
27	chr7:80549600-80551000	Enhancers	Duodenum Mucosa	Duodenum
28	chr7:80549600-80551000	Enhancers	HMEC	breast
29	chr7:80549600-80551800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr7:80549600-80552000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:80549600-80553600	Enhancers	Fetal Intestine Large	intestine
32	chr7:80549600-80553800	Enhancers	Fetal Intestine Small	intestine
33	chr7:80549600-80554000	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr7:80549800-80550000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:80549800-80550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:80549800-80550200	Weak transcription	Stomach Mucosa	stomach
37	chr7:80549800-80550200	Weak transcription	NHDF-Ad	bronchial
38	chr7:80549800-80550800	Weak transcription	Adipose Nuclei	Adipose
39	chr7:80549800-80551000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:80549800-80551600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:80549800-80552400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:80549800-80553800	Weak transcription	Colon Smooth Muscle	Colon

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