Variant report

Variant	rs7174089
Chromosome Location	chr15:83514473-83514474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83514448..83517408-chr15:83618486..83620458,2	MCF-7	breast:
2	chr15:83508986..83511908-chr15:83514316..83517080,4	K562	blood:
3	chr15:83508487..83510185-chr15:83513941..83516766,2	MCF-7	breast:
4	chr15:83512902..83515522-chr15:83653664..83656451,2	MCF-7	breast:
5	chr15:83513085..83515772-chr15:83516895..83519209,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169612	Chromatin interaction
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11259951	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11635618	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856316	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11856878	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs12903359	0.95[ASN][1000 genomes]
rs12905388	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs12910606	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17158263	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1828510	0.81[ASN][1000 genomes]
rs2046071	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]
rs2379994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34541883	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35788008	0.87[ASN][1000 genomes]
rs4778691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182990	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8042254	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9806482	0.88[AMR][1000 genomes];0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7174089	ARNT2	cis	cerebellum	SCAN
rs7174089	CHRNA5	cis	parietal	SCAN
rs7174089	WHAMM	cis	parietal	SCAN
rs7174089	GOLGA6L9	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83500400-83517600	Weak transcription	Fetal Heart	heart
2	chr15:83503600-83518200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:83503600-83518600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:83503600-83518600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
6	chr15:83505000-83518200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:83505800-83520800	Weak transcription	Dnd41	blood
8	chr15:83505800-83522400	Weak transcription	Fetal Kidney	kidney
9	chr15:83506000-83514600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:83506000-83518400	Weak transcription	NH-A	brain
11	chr15:83506000-83524200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:83506200-83518400	Weak transcription	NHDF-Ad	bronchial
13	chr15:83506200-83518800	Weak transcription	Brain Angular Gyrus	brain
14	chr15:83506200-83527400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:83506400-83518200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:83506400-83518600	Weak transcription	Ovary	ovary
18	chr15:83506400-83518800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:83506600-83518200	Weak transcription	Right Ventricle	heart
20	chr15:83506800-83518200	Weak transcription	A549	lung
21	chr15:83507000-83514600	Weak transcription	Placenta	Placenta
22	chr15:83507000-83515200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:83507000-83517000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:83507000-83518000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:83507000-83518200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:83507000-83518200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:83507000-83518600	Weak transcription	Spleen	Spleen
28	chr15:83507200-83518000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:83507200-83518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:83507200-83518200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:83507200-83518200	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:83507200-83518200	Weak transcription	Esophagus	oesophagus
33	chr15:83507200-83518600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
35	chr15:83507400-83515400	Weak transcription	Brain Anterior Caudate	brain
36	chr15:83507400-83516600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:83507400-83516800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:83507400-83517200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:83507400-83518000	Weak transcription	NHLF	lung
40	chr15:83507400-83518200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:83507400-83518800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:83507600-83514800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:83507600-83514800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:83507600-83516400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:83507600-83517200	Weak transcription	Adipose Nuclei	Adipose
46	chr15:83507600-83518000	Weak transcription	Fetal Lung	lung
47	chr15:83507600-83518000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:83507600-83518200	Weak transcription	Fetal Brain Female	brain
49	chr15:83507600-83518400	Weak transcription	Osteobl	bone
50	chr15:83507800-83516400	Weak transcription	HSMM	muscle

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