Variant report

Variant	rs11770880
Chromosome Location	chr7:100145928-100145929
allele	G/T
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	SPI1	chr7:100145497-100145975	GM12891	blood:	n/a	chr7:100145728-100145741
2	USF1	chr7:100145500-100145952	SK-N-SH	brain:	n/a	chr7:100145736-100145757
3	POLR2A	chr7:100145859-100146089	HepG2	liver:	n/a	n/a
4	USF1	chr7:100145550-100145955	ECC-1	luminal epithelium:	n/a	chr7:100145736-100145757
5	STAT1	chr7:100145587-100145950	K562	blood:	n/a	chr7:100145756-100145764 chr7:100145753-100145767
6	REST	chr7:100145584-100145949	K562	blood:	n/a	n/a
7	MTA3	chr7:100140880-100145936	GM12878	blood:	n/a	n/a
8	STAT5A	chr7:100145473-100145957	K562	blood:	n/a	chr7:100145756-100145764 chr7:100145753-100145767
9	POLR2A	chr7:100145085-100146623	HepG2	liver:	n/a	n/a
10	TEAD4	chr7:100145105-100145968	K562	blood:	n/a	n/a
11	JUN	chr7:100141383-100146123	K562	blood:	n/a	chr7:100144782-100144791 chr7:100143542-100143553 chr7:100143380-100143390 chr7:100143785-100143794 chr7:100143539-100143551 chr7:100143380-100143390 chr7:100143541-100143549 chr7:100143780-100143789 chr7:100143784-100143793 chr7:100141512-100141521 chr7:100142309-100142318 chr7:100143789-100143798 chr7:100142362-100142371 chr7:100143781-100143790 chr7:100143524-100143536
12	MAX	chr7:100145496-100145949	K562	blood:	n/a	chr7:100145742-100145751 chr7:100145742-100145751 chr7:100145741-100145752
13	SPI1	chr7:100145504-100145929	HL-60	blood:	n/a	chr7:100145728-100145741
14	POLR2A	chr7:100144997-100145990	HUVEC	blood vessel:	n/a	n/a
15	USF1	chr7:100145446-100146054	K562	blood:	n/a	chr7:100145736-100145757
16	POLR2A	chr7:100140894-100145981	HepG2	liver:	n/a	n/a
17	STAT1	chr7:100145574-100145934	K562	blood:	n/a	chr7:100145756-100145764 chr7:100145753-100145767
18	CTCF	chr7:100145780-100145930	HAc	cerebellar:	n/a	n/a
19	ELF1	chr7:100145518-100145942	K562	blood:	n/a	n/a
20	USF1	chr7:100145519-100145963	SK-N-SH_RA	brain:	n/a	chr7:100145736-100145757

No.	Distal block	Cell Line	Cell type
1	chr7:100025881..100027667-chr7:100143251..100146330,4	MCF-7	breast:
2	chr7:100140983..100146932-chr7:100182357..100186194,10	MCF-7	breast:
3	chr7:100144116..100146517-chr7:100289943..100291876,2	K562	blood:
4	chr7:100142841..100146326-chr7:100160207..100163065,3	MCF-7	breast:
5	chr7:100145746..100147750-chr7:100180240..100183063,2	K562	blood:
6	chr7:100145586..100147127-chr7:100152126..100154333,2	K562	blood:
7	chr7:100145206..100146855-chr7:100182658..100185253,2	K562	blood:
8	chr7:100144895..100147255-chr7:100148488..100151702,4	K562	blood:
9	chr7:100074335..100078343-chr7:100142686..100146158,4	K562	blood:
10	chr7:100067039..100069939-chr7:100143624..100146249,2	K562	blood:
11	chr7:100076149..100078056-chr7:100145849..100148358,2	MCF-7	breast:
12	chr7:100144343..100147077-chr7:100156607..100158371,2	MCF-7	breast:
13	chr7:100030016..100034371-chr7:100142404..100146654,4	K562	blood:

Variant related genes	Relation type
AGFG2	TF binding region
ENSG00000106351	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000241357	Chromatin interaction
ENSG00000166925	Chromatin interaction
ENSG00000240211	Chromatin interaction
ENSG00000146834	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11760595	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]
rs11761260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap]
rs2686815	0.86[JPT][hapmap]
rs34183059	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs35257323	0.82[JPT][hapmap]
rs3807475	0.82[JPT][hapmap]
rs4727456	0.82[JPT][hapmap]
rs5015755	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
4	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
5	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
6	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
7	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
8	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
9	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
10	nsv971157	chr7:100143688-100148402	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11770880	ZSCAN21	cis	parietal	SCAN
rs11770880	MOGAT3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100137800-100146600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:100138200-100146400	Weak transcription	Fetal Brain Female	brain
3	chr7:100138400-100146400	Weak transcription	Dnd41	blood
4	chr7:100140000-100148000	Enhancers	Primary B cells from peripheral blood	blood
5	chr7:100140400-100146200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:100141000-100146000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr7:100141000-100146600	Enhancers	Brain Cingulate Gyrus	brain
8	chr7:100141200-100146200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:100141200-100146600	Enhancers	Small Intestine	intestine
10	chr7:100141600-100146200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr7:100141600-100146400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr7:100141600-100146600	Enhancers	Fetal Heart	heart
13	chr7:100141800-100146200	Enhancers	Fetal Muscle Leg	muscle
14	chr7:100141800-100146400	Enhancers	Left Ventricle	heart
15	chr7:100141800-100146600	Enhancers	Adipose Nuclei	Adipose
16	chr7:100141800-100146600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr7:100141800-100147000	Enhancers	Right Atrium	heart
18	chr7:100141800-100147000	Enhancers	Stomach Mucosa	stomach
19	chr7:100142000-100146600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:100142000-100147000	Enhancers	Placenta	Placenta
21	chr7:100142400-100146200	Enhancers	Fetal Stomach	stomach
22	chr7:100142400-100146200	Enhancers	NHDF-Ad	bronchial
23	chr7:100142400-100146400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:100142400-100146400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr7:100142400-100146600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:100142600-100148600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:100142800-100146600	Enhancers	Right Ventricle	heart
28	chr7:100142800-100146800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr7:100142800-100147200	Enhancers	Spleen	Spleen
30	chr7:100143200-100146600	Enhancers	Pancreas	Pancrea
31	chr7:100143400-100146600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:100143600-100147400	Enhancers	Primary T cells from cord blood	blood
33	chr7:100144000-100146000	Flanking Active TSS	K562	blood
34	chr7:100144000-100146200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr7:100144000-100146400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr7:100144000-100146600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:100144000-100147000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:100144000-100150000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr7:100144200-100146200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:100144200-100146600	Enhancers	Osteobl	bone
41	chr7:100144200-100146800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:100144200-100146800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:100144200-100147000	Enhancers	Ovary	ovary
44	chr7:100144200-100151400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:100144200-100151600	Weak transcription	NHEK	skin
46	chr7:100144200-100167000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:100144400-100146000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:100144400-100146600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:100144400-100147000	Enhancers	Brain Anterior Caudate	brain
50	chr7:100144400-100147400	Weak transcription	Thymus	Thymus

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