Variant report

Variant	rs394845
Chromosome Location	chr15:59027671-59027672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59023017..59026002-chr15:59026211..59028184,2	K562	blood:
2	chr15:59026224..59028266-chr15:59062412..59064795,2	MCF-7	breast:
3	chr15:59025699..59027960-chr15:59038496..59040906,2	K562	blood:
4	chr15:59025073..59028168-chr15:59040901..59043745,3	K562	blood:

Variant related genes	Relation type
ENSG00000137845	Chromatin interaction
ENSG00000128923	Chromatin interaction
ENSG00000245975	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10851639	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11071396	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs11852241	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12437552	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[ASN][1000 genomes]
rs12439189	0.89[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap]
rs1427280	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17236243	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2114573	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2414606	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2414607	0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28391588	0.96[GIH][hapmap];0.86[MEX][hapmap]
rs3933541	0.82[ASN][1000 genomes]
rs406699	0.80[EUR][1000 genomes]
rs447299	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774309	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs655348	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs681711	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs694335	0.87[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7168275	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7173286	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7176436	0.86[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap]
rs7179724	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs7182060	0.87[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs8027998	0.96[GIH][hapmap];0.86[MEX][hapmap]
rs8036097	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs9646204	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs394845	CCPG1	cis	cerebellum	SCAN
rs394845	PYGO1	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:59008600-59028400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:59009600-59029600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:59009800-59035400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:59010800-59031200	Weak transcription	Dnd41	blood
6	chr15:59013200-59030200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:59013400-59029800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:59016800-59034200	Weak transcription	Brain Germinal Matrix	brain
9	chr15:59017200-59034400	Weak transcription	Fetal Kidney	kidney
10	chr15:59017400-59029000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:59021800-59029000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:59021800-59029600	Weak transcription	Fetal Lung	lung
13	chr15:59022000-59029600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr15:59022200-59040200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:59022400-59029400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:59022600-59034800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:59022600-59038600	Weak transcription	Fetal Brain Female	brain
18	chr15:59022800-59029600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:59023000-59030400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr15:59023600-59040000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr15:59023800-59028600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:59024000-59038200	Weak transcription	Fetal Stomach	stomach
23	chr15:59024200-59034600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:59024400-59028400	Weak transcription	Primary B cells from cord blood	blood
25	chr15:59024400-59029600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:59024400-59029800	Weak transcription	Hela-S3	cervix
27	chr15:59024400-59029800	Weak transcription	HUVEC	blood vessel
28	chr15:59024400-59030000	Weak transcription	NHLF	lung
29	chr15:59024400-59030600	Weak transcription	Ovary	ovary
30	chr15:59024400-59032400	Weak transcription	Lung	lung
31	chr15:59024400-59035200	Weak transcription	Fetal Muscle Leg	muscle
32	chr15:59024600-59029000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:59024600-59029600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:59024600-59029800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:59024600-59029800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:59024600-59029800	Weak transcription	HSMM	muscle
37	chr15:59024600-59031800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:59024600-59033200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:59024600-59034400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:59024800-59030000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:59025400-59028200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:59025400-59029600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:59025400-59029800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:59025400-59030200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:59025400-59030200	Weak transcription	NH-A	brain
46	chr15:59025400-59030400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:59025600-59028000	Enhancers	HMEC	breast
48	chr15:59025600-59029800	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:59025600-59029800	Weak transcription	NHDF-Ad	bronchial
50	chr15:59025600-59032200	Weak transcription	Placenta	Placenta

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