Variant report

Variant	rs718077
Chromosome Location	chr7:47798316-47798317
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	POLR2A	chr7:47797457-47798416	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:47797105-47798610	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr7:47797755-47798464	SK-N-SH_RA	brain:	n/a	chr7:47797919-47797929 chr7:47798003-47798017
4	RAD21	chr7:47797078-47799530	SK-N-SH	brain:	n/a	chr7:47798835-47798854 chr7:47798840-47798850 chr7:47797943-47797956 chr7:47798536-47798550
5	RAD21	chr7:47797797-47799472	SK-N-SH_RA	brain:	n/a	chr7:47798835-47798854 chr7:47798840-47798850 chr7:47797943-47797956 chr7:47798536-47798550
6	CTCF	chr7:47797844-47799078	A549	lung:	n/a	chr7:47798836-47798857 chr7:47798834-47798852 chr7:47798835-47798851 chr7:47798837-47798846

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47788868..47790580-chr7:47796478..47799163,2	MCF-7	breast:

Variant related genes	Relation type
LINC00525	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10245241	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10951925	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12536897	0.81[CHD][hapmap]
rs1453284	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1453285	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1597936	0.88[CHB][hapmap]
rs17627583	0.83[YRI][hapmap]
rs4339543	0.85[CHB][hapmap]
rs4724625	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4724626	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4724627	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4724629	0.81[AFR][1000 genomes]
rs4724631	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4724632	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4724633	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs718076	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1018608	chr7:47708525-47831535	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1022906	chr7:47709936-47831535	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015163	chr7:47734913-47832389	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv538831	chr7:47734913-47832389	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv830990	chr7:47767540-47837584	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs718077	GRB10	cis	parietal	SCAN
rs718077	LOC100129427	cis	cerebellum	SCAN
rs718077	HUS1	cis	cerebellum	SCAN
rs718077	HUS1	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47774400-47802600	Weak transcription	Pancreas	Pancrea
2	chr7:47796200-47798600	Enhancers	NH-A	brain
3	chr7:47796200-47799000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:47796200-47799000	Enhancers	Osteobl	bone
5	chr7:47796400-47799400	Enhancers	HMEC	breast
6	chr7:47796800-47799400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:47797000-47798400	Enhancers	Psoas Muscle	Psoas
8	chr7:47797000-47798600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:47797000-47798600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr7:47797200-47798400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:47797200-47798400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr7:47797200-47798400	Enhancers	Fetal Lung	lung
13	chr7:47797200-47798400	Enhancers	Fetal Muscle Leg	muscle
14	chr7:47797200-47798600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:47797200-47798600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:47797200-47798600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:47797200-47798600	Enhancers	Adipose Nuclei	Adipose
18	chr7:47797200-47798600	Enhancers	Aorta	Aorta
19	chr7:47797200-47798600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr7:47797200-47798600	Enhancers	Ovary	ovary
21	chr7:47797200-47798600	Enhancers	Right Atrium	heart
22	chr7:47797200-47798600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr7:47797200-47798800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:47797200-47799000	Enhancers	NHDF-Ad	bronchial
25	chr7:47797200-47799400	Enhancers	NHLF	lung
26	chr7:47797200-47799600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:47797200-47799600	Enhancers	A549	lung
28	chr7:47797400-47798400	Enhancers	Fetal Kidney	kidney
29	chr7:47797400-47798600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:47797400-47798600	Enhancers	Fetal Muscle Trunk	muscle
31	chr7:47797600-47798600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:47797600-47798600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr7:47797600-47798800	Enhancers	HepG2	liver
34	chr7:47797600-47799000	Enhancers	Hela-S3	cervix
35	chr7:47797800-47798400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:47797800-47798600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:47797800-47798600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr7:47797800-47798600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:47797800-47798600	Flanking Active TSS	HSMM	muscle
40	chr7:47797800-47802400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:47797800-47802800	Weak transcription	Placenta	Placenta
42	chr7:47798000-47798600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:47798000-47798800	Flanking Active TSS	HSMMtube	muscle
44	chr7:47798000-47803000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr7:47798200-47798600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:47798200-47798600	Enhancers	Esophagus	oesophagus
47	chr7:47798200-47802400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:47798200-47802600	Weak transcription	Placenta Amnion	Placenta Amnion

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