Variant report

Variant	rs10775122
Chromosome Location	chr15:41898711-41898712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41897965..41900106-chr15:41951801..41954247,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10152332	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10152364	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10775124	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1081022	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs11070345	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11070347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11632100	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11634840	0.81[AMR][1000 genomes]
rs11639146	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11639249	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12900295	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12902548	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12915325	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12916525	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1867416	0.86[AMR][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1899820	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs2141141	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2250964	0.86[AMR][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2577953	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2605570	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs2695169	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs4244585	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4270151	0.83[AMR][1000 genomes]
rs4371125	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4924571	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62002067	0.83[AMR][1000 genomes]
rs62002069	0.89[AMR][1000 genomes]
rs6493008	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493010	0.82[AMR][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7169668	0.86[AMR][1000 genomes]
rs7176474	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7177232	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8027390	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8028886	0.81[AMR][1000 genomes]
rs8030179	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8034261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8038148	1.00[JPT][hapmap]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10775122	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs10775122	ZSCAN29	cis	cerebellum	SCAN
rs10775122	TMEM87A	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41896600-41899600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:41896800-41899200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:41896800-41899200	Weak transcription	HSMM	muscle
4	chr15:41896800-41899400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:41897000-41899000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:41897000-41899200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:41897000-41899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:41897000-41899200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:41897000-41899200	Weak transcription	HMEC	breast
10	chr15:41897000-41899200	Weak transcription	NHEK	skin
11	chr15:41897000-41902200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:41897000-41902400	Weak transcription	HSMMtube	muscle
13	chr15:41897200-41899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:41897200-41899200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:41897200-41899200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:41897200-41899200	Weak transcription	NHDF-Ad	bronchial
17	chr15:41897200-41899600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:41897200-41900000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:41897200-41902000	Weak transcription	K562	blood
20	chr15:41897400-41900000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:41897800-41899200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:41898000-41899200	Weak transcription	NH-A	brain
23	chr15:41898000-41899200	Weak transcription	Osteobl	bone
24	chr15:41898200-41899200	Weak transcription	NHLF	lung
25	chr15:41898400-41898800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:41898600-41899800	Weak transcription	Placenta	Placenta

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