Variant report

Variant	rs12440747
Chromosome Location	chr15:42036690-42036691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42035386..42037537-chr15:42041123..42043627,2	MCF-7	breast:
2	chr15:42019750..42022278-chr15:42036338..42038977,2	K562	blood:
3	chr15:42028588..42031786-chr15:42034789..42036907,3	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1105881	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs1107858	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes]
rs11632424	0.88[EUR][1000 genomes]
rs11634956	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs11635067	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11635415	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11637341	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441300	0.82[EUR][1000 genomes]
rs1531140	0.96[CEU][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16952372	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs16971976	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs17676742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17677199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17677991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17678138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17678552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17678767	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs17734856	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1918310	0.96[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2004162	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2241522	0.96[CEU][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2277535	0.96[CEU][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303516	0.96[CEU][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2303518	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305654	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs2412622	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412641	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2577960	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28373318	0.82[EUR][1000 genomes]
rs28401754	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28432037	0.82[EUR][1000 genomes]
rs28444909	0.87[EUR][1000 genomes]
rs28451764	0.82[EUR][1000 genomes]
rs28556632	0.81[ASN][1000 genomes]
rs28680296	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28701757	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28754734	0.89[EUR][1000 genomes]
rs28810086	0.81[ASN][1000 genomes]
rs28850384	0.81[ASN][1000 genomes]
rs3179542	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3743024	0.96[CEU][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4923905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923910	0.88[AFR][1000 genomes]
rs4923914	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4923915	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924564	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4924570	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924575	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs4924576	0.96[CEU][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62002066	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62002090	0.85[EUR][1000 genomes]
rs62002091	0.85[EUR][1000 genomes]
rs62003900	0.81[ASN][1000 genomes]
rs7171123	0.92[ASN][1000 genomes]
rs8025714	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8035855	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs890498	0.81[EUR][1000 genomes]
rs890505	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9672298	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9672360	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9920903	0.90[EUR][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	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1048655	chr15:41978391-42049360	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1041861	chr15:42016097-42062287	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1044347	chr15:42023805-42049360	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12440747	MGA	cis	lesional skin	skin_eQTL
rs12440747	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:41989000-42041600	Weak transcription	Fetal Brain Male	brain
3	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
4	chr15:42006400-42041400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:42009800-42056800	Weak transcription	Fetal Heart	heart
6	chr15:42017400-42062600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:42019000-42037000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42019200-42037200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:42019400-42036800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:42019400-42037000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:42019400-42060600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:42020600-42037000	Strong transcription	Hela-S3	cervix
13	chr15:42021000-42036800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:42022400-42036800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:42023800-42037000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:42023800-42037200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:42024000-42036800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr15:42024000-42037000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:42024000-42037200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:42024600-42037000	Strong transcription	Placenta	Placenta
21	chr15:42025000-42045800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:42025400-42037200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:42025600-42037000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:42025800-42045000	Weak transcription	Stomach Mucosa	stomach
26	chr15:42027000-42037800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:42028800-42041200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:42029000-42041400	Weak transcription	Aorta	Aorta
29	chr15:42029000-42052200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:42029000-42054200	Weak transcription	Small Intestine	intestine
31	chr15:42029200-42041400	Weak transcription	NHDF-Ad	bronchial
32	chr15:42029200-42041600	Weak transcription	HMEC	breast
33	chr15:42029200-42048400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:42029400-42040800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:42030000-42038200	Weak transcription	HUVEC	blood vessel
36	chr15:42030400-42046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:42032200-42037000	Strong transcription	Primary B cells from cord blood	blood
38	chr15:42032600-42041400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:42033600-42037200	Strong transcription	Fetal Intestine Small	intestine
40	chr15:42033800-42038800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr15:42034000-42036800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:42034000-42037200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr15:42034400-42037000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:42034400-42037000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:42034400-42037200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr15:42034600-42036800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:42034600-42036800	Strong transcription	Thymus	Thymus
48	chr15:42034600-42037000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:42034800-42037000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr15:42034800-42037400	Strong transcription	Liver	Liver

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