Variant report

Variant	rs11070389
Chromosome Location	chr15:43394316-43394317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43388815..43390634-chr15:43391926..43394516,2	K562	blood:
2	chr15:43389228..43394941-chr15:43395904..43400327,7	K562	blood:
3	chr15:43392607..43394491-chr15:43442865..43444779,2	K562	blood:
4	chr15:43392059..43394941-chr15:43396768..43399559,3	K562	blood:
5	chr15:43392028..43394734-chr15:43397894..43400122,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159459	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10851414	0.89[ASN][1000 genomes]
rs11070385	0.87[EUR][1000 genomes]
rs11070390	0.89[ASN][1000 genomes]
rs11631404	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632120	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1197533	1.00[CEU][hapmap]
rs12050604	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1206698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs12437637	1.00[CEU][hapmap]
rs12442190	0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs12913112	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913213	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1474200	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1814323	1.00[ASW][hapmap]
rs2056346	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2139651	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2139652	0.89[ASN][1000 genomes]
rs2277532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs28418723	1.00[YRI][hapmap]
rs476342	0.83[ASN][1000 genomes]
rs489964	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap]
rs4923956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924702	0.81[EUR][1000 genomes]
rs502157	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.82[MKK][hapmap]
rs504417	1.00[ASW][hapmap]
rs513970	1.00[ASW][hapmap]
rs525403	0.82[CHB][hapmap]
rs530118	1.00[ASW][hapmap];0.82[CHD][hapmap];0.82[MKK][hapmap]
rs574856	0.84[ASN][1000 genomes]
rs62020706	0.87[EUR][1000 genomes]
rs7165861	0.89[ASN][1000 genomes]
rs7166467	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7169603	0.86[EUR][1000 genomes]
rs7176915	0.87[EUR][1000 genomes]
rs7496079	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8028822	0.82[EUR][1000 genomes]
rs9635327	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv904138	chr15:43268970-43414673	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
11	nsv904142	chr15:43276345-43403955	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv904143	chr15:43276345-43414673	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
14	nsv904146	chr15:43294218-43414673	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv904147	chr15:43309429-43403955	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11070389	TGM5	cis	lymphoblastoid	seeQTL
rs11070389	CCNDBP1	cis	multi-tissue	Pritchard
rs11070389	ADAL	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43269200-43397200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:43303400-43397400	Weak transcription	Esophagus	oesophagus
3	chr15:43346800-43395400	Weak transcription	Small Intestine	intestine
4	chr15:43348400-43397400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:43353000-43397400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:43367400-43394400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:43373200-43397200	Weak transcription	Fetal Brain Male	brain
8	chr15:43373600-43396600	Weak transcription	Pancreas	Pancrea
9	chr15:43375400-43396600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:43375600-43395400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:43376600-43397200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:43376800-43396400	Weak transcription	Fetal Kidney	kidney
13	chr15:43376800-43396600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:43377600-43397200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:43377600-43397200	Weak transcription	Colonic Mucosa	Colon
16	chr15:43379000-43396600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:43379200-43395800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:43382200-43396600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:43385800-43397400	Weak transcription	Lung	lung
20	chr15:43386000-43397400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:43386000-43397400	Weak transcription	Aorta	Aorta
22	chr15:43386000-43397400	Weak transcription	Ovary	ovary
23	chr15:43386200-43396200	Weak transcription	GM12878-XiMat	blood
24	chr15:43386400-43396600	Weak transcription	Left Ventricle	heart
25	chr15:43386600-43396600	Weak transcription	Right Ventricle	heart
26	chr15:43388000-43396600	Weak transcription	A549	lung
27	chr15:43388800-43394400	Weak transcription	Fetal Heart	heart
28	chr15:43388800-43397600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:43389200-43396000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:43389200-43396600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:43389600-43395600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:43389600-43395800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:43389600-43395800	Weak transcription	NHDF-Ad	bronchial
34	chr15:43390000-43397600	Weak transcription	Spleen	Spleen
35	chr15:43391000-43397200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:43391200-43395600	Strong transcription	Fetal Stomach	stomach
37	chr15:43391200-43396600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:43391200-43396600	Weak transcription	Brain Substantia Nigra	brain
39	chr15:43391400-43394800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:43391600-43394800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:43391600-43395000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:43391800-43394600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr15:43391800-43394600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr15:43391800-43394600	Strong transcription	Placenta	Placenta
45	chr15:43391800-43394600	Strong transcription	Fetal Thymus	thymus
46	chr15:43391800-43394800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:43391800-43394800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:43391800-43395000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:43391800-43395000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:43391800-43395400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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