Variant report

Variant	rs189497
Chromosome Location	chr15:74537101-74537102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74525638..74529372-chr15:74534834..74537226,3	K562	blood:
2	chr15:74535160..74537354-chr15:74542878..74545726,2	K562	blood:
3	chr15:74531319..74532959-chr15:74536975..74539724,2	MCF-7	breast:
4	chr15:74530832..74532774-chr15:74536942..74538994,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140481	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11629834	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11632233	0.80[CEU][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11633101	0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11633321	0.88[ASN][1000 genomes]
rs11638601	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639316	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs11858661	0.86[JPT][hapmap];0.84[MEX][hapmap]
rs12898529	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12904523	0.86[ASN][1000 genomes]
rs12905224	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905234	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905362	0.89[ASN][1000 genomes]
rs12913344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913651	0.80[CEU][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1564784	0.82[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs168432	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351152	0.95[AFR][1000 genomes]
rs351153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351160	0.82[JPT][hapmap]
rs351174	0.86[ASN][1000 genomes]
rs351180	0.83[ASN][1000 genomes]
rs351181	0.83[ASN][1000 genomes]
rs3848162	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs901128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv904349	chr15:74500105-74542686	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv904350	chr15:74500105-74548773	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs189497	SCAMP2	cis	cerebellum	SCAN
rs189497	ERP44	trans	cerebellum	SCAN
rs189497	MYO9A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74531400-74537600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:74531600-74538400	Enhancers	Spleen	Spleen
3	chr15:74532400-74537600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:74532600-74537600	Weak transcription	GM12878-XiMat	blood
5	chr15:74532800-74543200	Weak transcription	Psoas Muscle	Psoas
6	chr15:74533000-74537200	Weak transcription	Brain Anterior Caudate	brain
7	chr15:74533000-74537400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:74533000-74537400	Weak transcription	Brain Substantia Nigra	brain
9	chr15:74533400-74537600	Weak transcription	Esophagus	oesophagus
10	chr15:74533600-74537400	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:74533800-74537400	Weak transcription	Brain Angular Gyrus	brain
12	chr15:74535400-74537600	Weak transcription	Ovary	ovary
13	chr15:74535400-74537800	Weak transcription	HMEC	breast
14	chr15:74535400-74542200	Weak transcription	Right Atrium	heart
15	chr15:74535600-74537200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:74535600-74537200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:74535600-74537200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:74535600-74537200	Weak transcription	Lung	lung
19	chr15:74535600-74537400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:74535600-74537400	Weak transcription	HSMM	muscle
21	chr15:74535600-74537400	Weak transcription	NH-A	brain
22	chr15:74535600-74537600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:74535600-74537800	Weak transcription	Fetal Heart	heart
24	chr15:74535600-74537800	Weak transcription	Gastric	stomach
25	chr15:74535600-74537800	Weak transcription	Left Ventricle	heart
26	chr15:74535600-74542200	Weak transcription	HSMMtube	muscle
27	chr15:74535600-74543800	Weak transcription	Right Ventricle	heart
28	chr15:74535800-74537200	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:74535800-74537400	Weak transcription	Fetal Kidney	kidney
30	chr15:74536000-74537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:74536000-74537200	Weak transcription	Fetal Intestine Small	intestine
32	chr15:74536000-74537400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:74536000-74537400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr15:74536000-74537400	Weak transcription	Pancreas	Pancrea
35	chr15:74536200-74537400	Enhancers	Fetal Brain Female	brain
36	chr15:74536400-74537400	Enhancers	Brain Germinal Matrix	brain
37	chr15:74536400-74539200	Enhancers	Fetal Brain Male	brain
38	chr15:74536600-74537200	Enhancers	Hela-S3	cervix
39	chr15:74536600-74537400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:74536600-74537800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr15:74536800-74538400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr15:74536800-74538400	Enhancers	Fetal Thymus	thymus
43	chr15:74537000-74537600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:74537000-74537600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:74537000-74537800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
46	chr15:74537000-74537800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
47	chr15:74537000-74537800	Enhancers	Thymus	Thymus
48	chr15:74537000-74538400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr15:74537000-74538400	Bivalent Enhancer	Fetal Stomach	stomach
50	chr15:74537000-74538600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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