Variant report

Variant	rs7790887
Chromosome Location	chr7:80741161-80741162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:80740607..80742830-chr7:80744233..80747144,2	MCF-7	breast:
2	chr7:80722580..80725248-chr7:80741058..80743556,2	MCF-7	breast:
3	chr7:80740054..80742115-chr7:80745636..80747771,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10239474	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10245648	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10247169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10265624	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10270770	0.91[AFR][1000 genomes]
rs10274106	0.94[ASN][1000 genomes]
rs10277023	0.92[EUR][1000 genomes]
rs10277984	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534374	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs12538655	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12538859	0.80[TSI][hapmap]
rs12668893	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13240198	0.80[TSI][hapmap]
rs1528736	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17154740	0.80[TSI][hapmap]
rs2697219	0.92[EUR][1000 genomes]
rs2697221	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697222	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697224	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697225	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697227	0.84[ASN][1000 genomes]
rs2697943	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697944	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697945	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697946	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28627226	0.86[ASN][1000 genomes]
rs28715268	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28731315	0.82[ASN][1000 genomes]
rs34344876	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35876610	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4732106	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61059308	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6467564	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs6467574	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67243095	0.81[EUR][1000 genomes]
rs6955164	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6957232	0.86[CEU][hapmap];0.92[TSI][hapmap]
rs6959189	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6968574	0.82[AFR][1000 genomes]
rs6973162	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs949733	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953190	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv888552	chr7:80683308-80755310	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv888553	chr7:80683308-80766407	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv888554	chr7:80695828-80755310	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv888555	chr7:80695828-80766407	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv888556	chr7:80695828-80797794	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv831044	chr7:80721773-80918591	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7790887	SEMA3C	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80738400-80743400	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr7:80739800-80741400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:80739800-80741400	Enhancers	HMEC	breast
4	chr7:80739800-80741400	Enhancers	HSMM	muscle
5	chr7:80739800-80741600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:80739800-80742400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:80739800-80742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:80739800-80743200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:80740200-80741400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:80740200-80741400	Enhancers	Primary hematopoietic stem cells	blood
11	chr7:80740200-80741400	Enhancers	Fetal Lung	lung
12	chr7:80740200-80741400	Enhancers	NHDF-Ad	bronchial
13	chr7:80740200-80741600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr7:80740200-80741600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:80740200-80741800	Enhancers	NH-A	brain
16	chr7:80740200-80741800	Enhancers	Osteobl	bone
17	chr7:80740200-80742400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:80740200-80743600	Enhancers	Colon Smooth Muscle	Colon
19	chr7:80740400-80741200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:80740400-80741400	Enhancers	Rectal Smooth Muscle	rectum
21	chr7:80740800-80741200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:80740800-80741200	Enhancers	Stomach Smooth Muscle	stomach
23	chr7:80740800-80741400	Enhancers	HSMMtube	muscle
24	chr7:80740800-80741800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:80740800-80741800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:80740800-80742000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:80740800-80742600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:80741000-80741200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr7:80741000-80741200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr7:80741000-80741200	Enhancers	Brain Hippocampus Middle	brain
31	chr7:80741000-80741400	Enhancers	Brain Anterior Caudate	brain
32	chr7:80741000-80741400	Enhancers	Brain Cingulate Gyrus	brain
33	chr7:80741000-80741400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr7:80741000-80741400	Enhancers	Fetal Kidney	kidney
35	chr7:80741000-80741400	Enhancers	NHLF	lung
36	chr7:80741000-80741600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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