Variant report

Variant	rs2046071
Chromosome Location	chr15:83507051-83507052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83477415..83480373-chr15:83506033..83507641,2	MCF-7	breast:
2	chr15:83477910..83479814-chr15:83506678..83508717,2	MCF-7	breast:
3	chr15:83417933..83421305-chr15:83506438..83509474,3	MCF-7	breast:
4	chr15:83501706..83503729-chr15:83505602..83507499,2	MCF-7	breast:
5	chr15:83502060..83506247-chr15:83506644..83510779,4	K562	blood:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction
ENSG00000156232	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11259951	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs11635618	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11856316	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11856878	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs12903359	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905388	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs12910606	0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs17158263	0.87[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2379994	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs34541883	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35788008	0.86[ASN][1000 genomes]
rs4778691	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174089	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182990	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042254	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9806482	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[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	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	hippocampus	BrainEAC
rs2046071	CHRNA5	cis	parietal	SCAN
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	frontal cortex	BrainEAC
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	intralobular white matter	BrainEAC
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	temporal cortex	BrainEAC
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	thalamus	BrainEAC
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	brain	BrainEAC
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	occipital cortex	BrainEAC
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	inferior olivary nucleus	BrainEAC
rs2046071	WHAMM	cis	parietal	SCAN
rs2046071	WHAMM,WHAMML1,WHAMML2	cis	cerebellar cortex	BrainEAC
rs2046071	ARNT2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83481200-83507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:83481800-83507600	Strong transcription	Adipose Nuclei	Adipose
3	chr15:83483200-83507400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:83491000-83508000	Strong transcription	Thymus	Thymus
5	chr15:83491200-83507400	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:83491400-83507400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:83491400-83507400	Strong transcription	Fetal Muscle Leg	muscle
8	chr15:83491400-83508200	Strong transcription	Left Ventricle	heart
9	chr15:83491800-83507600	Strong transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:83492000-83507400	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:83492200-83507400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:83493000-83507600	Strong transcription	Fetal Brain Female	brain
13	chr15:83493600-83507400	Strong transcription	Primary T cells from cord blood	blood
14	chr15:83493600-83507800	Strong transcription	Brain Germinal Matrix	brain
15	chr15:83493600-83508000	Strong transcription	Primary B cells from cord blood	blood
16	chr15:83494800-83507400	Strong transcription	Brain Substantia Nigra	brain
17	chr15:83496600-83507200	Strong transcription	Colon Smooth Muscle	Colon
18	chr15:83496600-83507800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:83500400-83517600	Weak transcription	Fetal Heart	heart
20	chr15:83500600-83507200	Strong transcription	Fetal Intestine Small	intestine
21	chr15:83501200-83507200	Strong transcription	Brain Cingulate Gyrus	brain
22	chr15:83501200-83508000	Strong transcription	Brain Hippocampus Middle	brain
23	chr15:83501400-83507200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:83501800-83507400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr15:83502000-83507200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:83502000-83507400	Strong transcription	Brain Anterior Caudate	brain
27	chr15:83502200-83507200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:83502200-83507200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:83502200-83507400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr15:83502200-83507400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:83502400-83507200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr15:83502400-83507400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:83502400-83507400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:83502400-83507400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:83502400-83507400	Strong transcription	Gastric	stomach
36	chr15:83502400-83507400	Strong transcription	Pancreas	Pancrea
37	chr15:83502400-83507400	Strong transcription	NHLF	lung
38	chr15:83502400-83507600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:83502400-83507600	Strong transcription	Liver	Liver
40	chr15:83502400-83507600	Strong transcription	Fetal Lung	lung
41	chr15:83502400-83507600	Strong transcription	Osteobl	bone
42	chr15:83502400-83507800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:83502400-83507800	Strong transcription	HSMM	muscle
44	chr15:83502400-83508000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:83502400-83508200	Strong transcription	HSMMtube	muscle
46	chr15:83502400-83508200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr15:83502400-83508600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr15:83502600-83507200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:83502600-83507600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:83502600-83507600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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