Variant report

Variant	rs11632100
Chromosome Location	chr15:41946620-41946621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41939277..41941005-chr15:41945553..41947159,2	MCF-7	breast:
2	chr15:41945176..41947724-chr15:41947900..41950145,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1008710	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs10152332	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152364	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775124	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap]
rs11070345	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634840	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639146	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11639249	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11855017	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs1197768	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197769	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900295	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902548	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12915325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916525	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1648833	1.00[CEU][hapmap]
rs1648834	1.00[CEU][hapmap]
rs1648835	1.00[CEU][hapmap]
rs1672465	1.00[CEU][hapmap]
rs1672466	1.00[CEU][hapmap]
rs16972089	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs16972136	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1867416	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880937	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880938	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009310	0.91[ASN][1000 genomes]
rs2141141	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250964	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577953	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605569	0.88[EUR][1000 genomes]
rs2605570	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695162	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695166	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695168	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2695169	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695170	0.90[EUR][1000 genomes]
rs2918051	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2950446	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270151	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924571	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002067	0.86[AMR][1000 genomes]
rs62002069	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493008	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493010	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164209	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169668	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176474	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177232	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027390	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028886	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030179	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038148	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11632100	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41925000-41952200	Weak transcription	Ovary	ovary
2	chr15:41927000-41951800	Weak transcription	Hela-S3	cervix
3	chr15:41940000-41947800	Weak transcription	Dnd41	blood
4	chr15:41941000-41951400	Weak transcription	Fetal Kidney	kidney
5	chr15:41941200-41952000	Weak transcription	HSMM	muscle
6	chr15:41941600-41947200	Weak transcription	Osteobl	bone
7	chr15:41941600-41952000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:41941600-41952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:41941800-41947600	Weak transcription	NH-A	brain
10	chr15:41943400-41952000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:41944800-41948400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:41945200-41946800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:41945600-41947000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr15:41946000-41946800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr15:41946000-41946800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr15:41946400-41947400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:41946400-41951400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:41946400-41952000	Weak transcription	Spleen	Spleen
19	chr15:41946600-41946800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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