Variant report

Variant	rs4244585
Chromosome Location	chr15:41941111-41941112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41939185..41941981-chr15:41952544..41954491,2	MCF-7	breast:
2	chr15:41926831..41929447-chr15:41939833..41942397,2	K562	blood:
3	chr15:41938340..41941211-chr15:41951794..41954660,3	K562	blood:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10152332	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10152364	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775122	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]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775124	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs11070345	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11632100	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11634840	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11639146	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11639249	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11855017	0.80[EUR][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs1197769	0.81[EUR][1000 genomes]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12900295	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902548	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12915325	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916525	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1648833	1.00[CEU][hapmap];0.91[MEX][hapmap]
rs1648834	1.00[CEU][hapmap]
rs1648835	1.00[CEU][hapmap];0.91[MEX][hapmap]
rs1672465	1.00[CEU][hapmap]
rs1672466	1.00[CEU][hapmap]
rs16972089	0.93[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs16972136	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs1867416	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1880937	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1880938	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1899820	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs2141141	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2250964	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2577953	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577955	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577958	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2605569	0.86[EUR][1000 genomes]
rs2605570	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2695162	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695166	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2695168	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2695169	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695170	0.88[EUR][1000 genomes]
rs2918051	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2950446	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4270151	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924571	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62002067	0.88[AMR][1000 genomes]
rs62002069	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6493008	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493010	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7164209	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7169668	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176474	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177232	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8027390	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8028886	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8030179	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8034261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4244585	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs4244585	TMEM87A	cis	cerebellum	SCAN
rs4244585	ZSCAN29	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr15:41931200-41941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:41933200-41945000	Weak transcription	Right Atrium	heart
5	chr15:41939000-41941200	Weak transcription	Psoas Muscle	Psoas
6	chr15:41939000-41942000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:41939200-41941800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr15:41939400-41941200	Enhancers	Fetal Intestine Large	intestine
9	chr15:41939400-41941400	Enhancers	HepG2	liver
10	chr15:41939600-41941200	Enhancers	HSMM	muscle
11	chr15:41939600-41941800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:41940000-41942800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:41940000-41947800	Weak transcription	Dnd41	blood
14	chr15:41940200-41941200	Enhancers	Liver	Liver
15	chr15:41940400-41941200	Enhancers	Brain Substantia Nigra	brain
16	chr15:41940400-41941200	Enhancers	NHLF	lung
17	chr15:41940400-41941400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:41940400-41941400	Enhancers	NHDF-Ad	bronchial
19	chr15:41940600-41941400	Enhancers	HMEC	breast
20	chr15:41940600-41942000	Weak transcription	A549	lung
21	chr15:41940800-41941200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:41940800-41941200	Enhancers	NHEK	skin
23	chr15:41940800-41941400	Flanking Active TSS	Osteobl	bone
24	chr15:41940800-41941600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:41940800-41941600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:41940800-41941600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:41941000-41941400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:41941000-41941400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:41941000-41941400	Flanking Active TSS	NH-A	brain
30	chr15:41941000-41951400	Weak transcription	Fetal Kidney	kidney

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