Variant report

Variant	rs12913651
Chromosome Location	chr15:74531418-74531419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74530832..74532774-chr15:74536942..74538994,3	MCF-7	breast:
2	chr15:74531000..74533096-chr15:74589038..74591277,2	MCF-7	breast:
3	chr15:74531319..74532959-chr15:74536975..74539724,2	MCF-7	breast:
4	chr15:74531065..74532057-chr7:5566416..5567064,2	Hela-S3	cervix:
5	chr15:74531244..74533706-chr15:74533938..74535590,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11629834	0.80[CEU][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11632233	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11633101	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11633321	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638601	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11639316	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12898529	0.85[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12904523	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905224	0.86[ASN][1000 genomes]
rs12905234	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12905362	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12913344	0.80[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1564784	0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs168432	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs189497	0.80[CEU][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs351153	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs351159	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs351174	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351175	0.86[JPT][hapmap]
rs351178	0.81[JPT][hapmap]
rs351180	0.92[ASN][1000 genomes]
rs351181	0.92[ASN][1000 genomes]
rs368416	0.80[JPT][hapmap]
rs3848162	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs392267	0.81[JPT][hapmap]
rs6495091	0.82[JPT][hapmap];0.81[TSI][hapmap]
rs67882706	0.86[ASN][1000 genomes]
rs901128	0.83[CEU][hapmap];0.85[CHB][hapmap];0.80[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
rs12913651	CELF6	cis	parietal	SCAN
rs12913651	CORO2B	cis	parietal	SCAN
rs12913651	SCAMP2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74526400-74531600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:74526600-74531800	Weak transcription	Fetal Lung	lung
3	chr15:74526600-74532000	Weak transcription	Esophagus	oesophagus
4	chr15:74526800-74531600	Weak transcription	Placenta	Placenta
5	chr15:74526800-74531600	Weak transcription	Osteobl	bone
6	chr15:74527000-74531600	Weak transcription	HSMM	muscle
7	chr15:74527000-74531800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:74527000-74531800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:74527000-74531800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:74527200-74531600	Weak transcription	Fetal Brain Female	brain
11	chr15:74527200-74531600	Weak transcription	Spleen	Spleen
12	chr15:74527400-74531600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:74527400-74531800	Weak transcription	Right Atrium	heart
14	chr15:74528600-74532000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:74528600-74532600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr15:74528600-74536800	Weak transcription	Fetal Thymus	thymus
17	chr15:74528800-74532000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:74528800-74532200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:74529000-74532200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:74529000-74532200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:74529000-74532600	Weak transcription	Fetal Intestine Large	intestine
22	chr15:74529200-74531800	Weak transcription	Colonic Mucosa	Colon
23	chr15:74529200-74535400	Weak transcription	Fetal Kidney	kidney
24	chr15:74529800-74532000	Weak transcription	Fetal Intestine Small	intestine
25	chr15:74530800-74535800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:74531000-74531600	Enhancers	A549	lung
27	chr15:74531000-74532000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr15:74531000-74532800	Enhancers	Hela-S3	cervix
29	chr15:74531000-74533000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr15:74531000-74533200	Enhancers	Fetal Stomach	stomach
31	chr15:74531000-74535400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:74531000-74535600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:74531000-74536000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:74531000-74536000	Enhancers	Fetal Brain Male	brain
35	chr15:74531000-74536200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr15:74531200-74531800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr15:74531200-74532800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr15:74531200-74532800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:74531200-74533000	Enhancers	HSMMtube	muscle
40	chr15:74531200-74533200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr15:74531200-74533400	Enhancers	NH-A	brain
42	chr15:74531200-74534600	Enhancers	Fetal Muscle Leg	muscle
43	chr15:74531200-74535200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:74531400-74531600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr15:74531400-74532000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr15:74531400-74532600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:74531400-74532600	Enhancers	GM12878-XiMat	blood
48	chr15:74531400-74532800	Enhancers	Ovary	ovary
49	chr15:74531400-74533600	Enhancers	Brain Hippocampus Middle	brain
50	chr15:74531400-74533800	Enhancers	Gastric	stomach

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