Variant report

Variant	rs11630972
Chromosome Location	chr15:41993666-41993667
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	chr15:41966089..41968665-chr15:41992958..41994638,2	K562	blood:
2	chr15:41987207..41988924-chr15:41992415..41994588,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1122884	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs11631051	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11632519	1.00[JPT][hapmap]
rs11633160	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11634083	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs11634582	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11634804	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11636523	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1197667	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1197669	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs1197671	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1197672	0.96[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs1197703	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs1197705	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs12148570	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906666	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12917387	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17676332	1.00[JPT][hapmap]
rs17677098	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17677757	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17678310	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2178003	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2925339	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs34621600	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35665813	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714979	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61104950	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62003901	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167078	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175318	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040094	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042809	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9646193	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11630972	SPTBN5	cis	lung	GTEx
rs11630972	MAPKBP1	cis	cerebellum	SCAN
rs11630972	NDUFAF1	cis	parietal	SCAN
rs11630972	MAPKBP1	cis	parietal	SCAN
rs11630972	RPAP1	cis	parietal	SCAN
rs11630972	SPTBN5	cis	Artery Tibial	GTEx
rs11630972	SNAP23	cis	parietal	SCAN
rs11630972	SPTBN5	cis	cerebellum	SCAN
rs11630972	CAPN3	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
2	chr15:41962000-42001400	Weak transcription	Gastric	stomach
3	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:41971600-41997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:41972800-41999600	Weak transcription	Fetal Brain Female	brain
7	chr15:41981600-41995800	Weak transcription	Fetal Stomach	stomach
8	chr15:41983000-42001200	Weak transcription	Ovary	ovary
9	chr15:41983200-42002600	Weak transcription	Small Intestine	intestine
10	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:41984400-42002800	Weak transcription	A549	lung
12	chr15:41984600-41999200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:41984600-41999400	Weak transcription	Thymus	Thymus
14	chr15:41984600-41999800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:41984600-42000600	Weak transcription	Lung	lung
16	chr15:41984600-42001600	Weak transcription	Pancreas	Pancrea
17	chr15:41984800-41998800	Weak transcription	Left Ventricle	heart
18	chr15:41984800-41999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:41984800-42000800	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:41984800-42001200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:41984800-42001400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:41984800-42003000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:41985200-41996000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:41987600-42001200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:41988200-41995000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:41988600-42001200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:41988600-42003000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:41988600-42003000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:41988800-41994600	Strong transcription	Fetal Thymus	thymus
30	chr15:41988800-42002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:41988800-42003000	Weak transcription	Fetal Kidney	kidney
32	chr15:41989000-41997400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:41989000-41999000	Weak transcription	Fetal Lung	lung
34	chr15:41989000-42003000	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:41989000-42041600	Weak transcription	Fetal Brain Male	brain
36	chr15:41989200-41993800	Strong transcription	Primary T cells from cord blood	blood
37	chr15:41989200-41998800	Weak transcription	Dnd41	blood
38	chr15:41989200-41999400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:41989200-41999400	Weak transcription	Placenta	Placenta
40	chr15:41989200-42000400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:41989200-42000800	Weak transcription	Psoas Muscle	Psoas
42	chr15:41989200-42000800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:41989200-42001000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:41989200-42001000	Weak transcription	Brain Angular Gyrus	brain
45	chr15:41989200-42001000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:41989200-42001200	Weak transcription	Brain Anterior Caudate	brain
47	chr15:41989200-42001200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:41989200-42001200	Weak transcription	Right Ventricle	heart
49	chr15:41989200-42001600	Weak transcription	HSMMtube	muscle
50	chr15:41989200-42003000	Weak transcription	Brain Substantia Nigra	brain

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