Variant report

Variant	rs7896644
Chromosome Location	chr10:49764050-49764051
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49763447..49764254-chr10:49864053..49864628,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10491040	0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs10776614	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs10776615	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[ASN][1000 genomes]
rs10776616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857592	0.82[CHB][hapmap]
rs10857596	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10857598	0.87[ASN][1000 genomes]
rs11101368	0.82[CHB][hapmap]
rs11101377	0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[ASN][1000 genomes]
rs11101381	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11101382	1.00[CHB][hapmap]
rs11101384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358311	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12358315	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12412164	0.93[ASN][1000 genomes]
rs1345104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345109	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[ASN][1000 genomes]
rs1345110	0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[ASN][1000 genomes]
rs1345111	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[ASN][1000 genomes]
rs1348633	0.82[ASN][1000 genomes]
rs1445148	0.91[ASN][1000 genomes]
rs1473323	0.83[ASN][1000 genomes]
rs1814469	0.82[ASN][1000 genomes]
rs1838568	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1838569	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1838570	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[ASN][1000 genomes]
rs1838573	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs1838574	0.82[ASN][1000 genomes]
rs1838579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900021	0.80[ASN][1000 genomes]
rs1965170	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2077152	1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[ASN][1000 genomes]
rs2120910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4084916	0.87[ASN][1000 genomes]
rs4101278	0.80[ASN][1000 genomes]
rs4450130	0.82[CHB][hapmap]
rs4838418	0.82[ASN][1000 genomes]
rs4838421	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838422	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838617	0.93[ASN][1000 genomes]
rs4838623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058334	0.91[ASN][1000 genomes]
rs56080723	0.80[ASN][1000 genomes]
rs56248718	0.80[ASN][1000 genomes]
rs6537568	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7071095	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7071480	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7072237	0.82[ASN][1000 genomes]
rs7074631	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7085183	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7085335	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs7087729	1.00[CHB][hapmap]
rs7088010	0.91[ASN][1000 genomes]
rs7094216	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7096053	0.85[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs7098068	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7350424	0.91[ASN][1000 genomes]
rs7350439	0.91[ASN][1000 genomes]
rs747533	0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs7894707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7894971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7904456	0.91[ASN][1000 genomes]
rs7905247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935271	0.82[CHB][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7896644	A1CF	cis	cerebellum	SCAN
rs7896644	FRMPD2	cis	cerebellum	SCAN
rs7896644	FYN	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
2	chr10:49751200-49771600	Weak transcription	Pancreas	Pancrea
3	chr10:49753400-49764400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:49757400-49782200	Weak transcription	HSMMtube	muscle
5	chr10:49759200-49770400	Weak transcription	NH-A	brain
6	chr10:49759800-49764200	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr10:49760200-49764600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr10:49760800-49765000	Strong transcription	NHLF	lung
9	chr10:49760800-49765400	Strong transcription	HSMM	muscle
10	chr10:49760800-49765600	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr10:49760800-49768800	Weak transcription	Ovary	ovary
12	chr10:49761000-49764800	Strong transcription	Osteobl	bone
13	chr10:49761000-49765400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:49761400-49764400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:49761400-49765600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:49761600-49780600	Weak transcription	HUVEC	blood vessel
17	chr10:49761800-49765400	Strong transcription	NHDF-Ad	bronchial
18	chr10:49762000-49764400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:49762000-49764600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:49762000-49765600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr10:49762600-49772600	Weak transcription	Brain Angular Gyrus	brain
22	chr10:49762800-49764200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:49762800-49765400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:49762800-49765600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:49763200-49780800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr10:49763400-49764600	Strong transcription	HMEC	breast
27	chr10:49763800-49772600	Weak transcription	Brain Substantia Nigra	brain

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