Variant report

Variant	rs7181178
Chromosome Location	chr15:92569957-92569958
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	chr15:92562839..92565166-chr15:92567346..92570436,4	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12593984	0.83[JPT][hapmap]
rs12899498	0.80[AMR][1000 genomes]
rs12899673	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12904266	0.83[JPT][hapmap]
rs12905838	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12905905	0.93[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs12905912	0.83[JPT][hapmap]
rs12906289	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12912272	0.82[JPT][hapmap]
rs12912997	0.83[JPT][hapmap]
rs12913189	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35000646	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57842850	0.94[ASN][1000 genomes]
rs62011580	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71411125	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163548	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7166185	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178378	0.83[JPT][hapmap]
rs8040010	0.83[JPT][hapmap]

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	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv984212	chr15:92562075-92570410	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7181178	CHD2	cis	cerebellum	SCAN
rs7181178	MAN2A2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92555600-92570600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr15:92555600-92576200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr15:92558000-92571200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:92562600-92570600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:92562800-92574600	Weak transcription	Esophagus	oesophagus
6	chr15:92564600-92570000	Enhancers	Brain Hippocampus Middle	brain
7	chr15:92564600-92571400	Weak transcription	Small Intestine	intestine
8	chr15:92565200-92571400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:92565200-92572000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:92565200-92573400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:92565400-92572400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:92566200-92570600	Weak transcription	Brain Angular Gyrus	brain
13	chr15:92566200-92570800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:92566200-92576400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:92567600-92571200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:92567600-92573000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:92567800-92570000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr15:92567800-92570600	Weak transcription	Adipose Nuclei	Adipose
19	chr15:92567800-92571600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:92568200-92571000	Weak transcription	Aorta	Aorta
21	chr15:92568200-92571400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:92568600-92571800	Enhancers	Right Ventricle	heart
23	chr15:92568800-92571200	Weak transcription	Fetal Brain Male	brain
24	chr15:92568800-92572400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:92569200-92570800	Weak transcription	Fetal Lung	lung
26	chr15:92569200-92572600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:92569400-92570800	Weak transcription	Lung	lung
28	chr15:92569400-92570800	Weak transcription	Ovary	ovary
29	chr15:92569400-92573000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:92569600-92570600	Weak transcription	Right Atrium	heart
31	chr15:92569600-92570600	Weak transcription	Spleen	Spleen
32	chr15:92569600-92570800	Weak transcription	Left Ventricle	heart
33	chr15:92569600-92571000	Weak transcription	Brain Substantia Nigra	brain
34	chr15:92569600-92571200	Weak transcription	Fetal Heart	heart
35	chr15:92569800-92573000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:92569800-92576600	Weak transcription	Brain Anterior Caudate	brain

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