Variant report

Variant	rs1081022
Chromosome Location	chr15:42075123-42075124
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42064976..42070217-chr15:42070811..42075517,5	K562	blood:
2	chr15:42066709..42068475-chr15:42073432..42076353,2	K562	blood:

Variant related genes	Relation type
ENSG00000137802	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1008710	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs1061354	0.82[EUR][1000 genomes]
rs10775122	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs10775123	1.00[CEU][hapmap]
rs11070347	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs11070350	0.86[EUR][1000 genomes]
rs11634840	0.88[EUR][1000 genomes]
rs11857301	0.99[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1197670	0.86[EUR][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1197768	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1197769	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1197772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12148330	1.00[CEU][hapmap]
rs12441249	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12915325	1.00[CEU][hapmap]
rs12916992	1.00[CEU][hapmap]
rs1648827	0.86[EUR][1000 genomes]
rs1648828	0.86[EUR][1000 genomes]
rs1648829	0.85[EUR][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1648831	0.86[EUR][1000 genomes]
rs1648832	0.86[EUR][1000 genomes]
rs1648833	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1648834	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1648835	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1672464	0.86[EUR][1000 genomes]
rs1672465	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1672466	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs16972089	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16972136	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs1867417	1.00[CEU][hapmap]
rs1880937	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1899819	1.00[CEU][hapmap]
rs1899820	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs1899821	1.00[CEU][hapmap]
rs1918314	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2178004	1.00[CEU][hapmap]
rs2577947	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2577950	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2577951	1.00[CEU][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2577952	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap]
rs2577955	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577959	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2605569	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2605570	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2695162	0.82[EUR][1000 genomes]
rs2695163	1.00[CEU][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2695164	1.00[CEU][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes]
rs2695165	0.81[ASN][1000 genomes]
rs2695169	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2925337	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3784282	0.84[EUR][1000 genomes]
rs4078788	0.84[EUR][1000 genomes]
rs4244585	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs4371125	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4465584	1.00[CEU][hapmap]
rs4923908	1.00[CEU][hapmap]
rs4924568	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs4924572	1.00[CEU][hapmap]
rs57498313	0.86[EUR][1000 genomes]
rs7164209	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7165230	0.86[EUR][1000 genomes]
rs7169496	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs7177911	1.00[CEU][hapmap]
rs7178205	1.00[CEU][hapmap]
rs8028886	0.90[EUR][1000 genomes]
rs8034261	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs8038783	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs890508	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	nsv1038894	chr15:42038152-42077452	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	19 gene(s)	inside rSNPs	diseases
9	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1081022	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs1081022	C17orf85	trans	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42067600-42083000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:42068000-42075200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:42068000-42078800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:42068200-42082600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:42068400-42075200	Weak transcription	Pancreas	Pancrea
6	chr15:42068400-42081800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:42068600-42081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:42069200-42075200	Weak transcription	K562	blood
9	chr15:42069400-42075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:42069800-42075200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:42069800-42075200	Weak transcription	Gastric	stomach
12	chr15:42069800-42081800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:42070000-42081600	Weak transcription	Aorta	Aorta
14	chr15:42070000-42082600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
16	chr15:42071000-42082400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:42071000-42082800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:42071000-42092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:42071200-42092000	Weak transcription	Brain Germinal Matrix	brain
20	chr15:42072400-42075600	Weak transcription	Lung	lung
21	chr15:42072400-42077400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:42072400-42080400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:42072400-42080800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:42072400-42081600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:42072600-42075200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:42072600-42075200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:42072600-42075200	Weak transcription	HSMM	muscle
28	chr15:42072600-42080600	Weak transcription	Primary T cells from cord blood	blood
29	chr15:42072600-42081200	Weak transcription	HSMMtube	muscle
30	chr15:42072600-42081800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:42072600-42081800	Weak transcription	NH-A	brain
32	chr15:42072600-42082600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:42072800-42075200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:42072800-42075200	Weak transcription	Spleen	Spleen
35	chr15:42072800-42080600	Weak transcription	Brain Anterior Caudate	brain
36	chr15:42072800-42080600	Weak transcription	Left Ventricle	heart
37	chr15:42072800-42080600	Weak transcription	Psoas Muscle	Psoas
38	chr15:42072800-42080600	Weak transcription	Right Ventricle	heart
39	chr15:42072800-42080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr15:42072800-42081600	Weak transcription	Right Atrium	heart
41	chr15:42073000-42075200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:42073000-42080800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:42073000-42081000	Weak transcription	Adipose Nuclei	Adipose
44	chr15:42073000-42081200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:42073000-42081400	Weak transcription	Fetal Stomach	stomach
46	chr15:42073000-42082600	Weak transcription	A549	lung
47	chr15:42073200-42075200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:42073200-42075600	Weak transcription	Stomach Mucosa	stomach
49	chr15:42073200-42080600	Weak transcription	Brain Angular Gyrus	brain
50	chr15:42073200-42080600	Weak transcription	Brain Cingulate Gyrus	brain

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