Variant report

Variant	rs12515399
Chromosome Location	chr5:179108502-179108503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr5:179108347-179108633	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:179108432-179108524	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179101962..179108661-chr5:179122383..179128408,19	MCF-7	breast:
2	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
3	chr5:179100989..179111182-chr5:179122076..179128627,19	K562	blood:
4	chr5:179047581..179051358-chr5:179102429..179108878,16	K562	blood:
5	chr5:179048156..179052144-chr5:179103013..179109071,12	K562	blood:

No data

Variant related genes	Relation type
CBY3	TF binding region
ENSG00000169045	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11249655	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249656	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11249657	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249658	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11749559	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11750523	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188238	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12518476	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28674071	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28846185	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34646062	0.81[JPT][hapmap]
rs55702506	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56159807	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60216315	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406697	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62406698	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67484565	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6879412	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7379093	0.80[ASN][1000 genomes]
rs7719302	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9637934	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9637935	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9763971	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12515399	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs12515399	PROP1	cis	parietal	SCAN
rs12515399	MAPK9	cis	cerebellum	SCAN
rs12515399	GRM6	cis	cerebellum	SCAN
rs12515399	CLTB	cis	parietal	SCAN
rs12515399	MAML1	cis	parietal	SCAN
rs12515399	CANX	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179106400-179118200	Weak transcription	Right Ventricle	heart
2	chr5:179106600-179108600	Enhancers	Primary T cells from cord blood	blood
3	chr5:179106600-179108600	Enhancers	Duodenum Mucosa	Duodenum
4	chr5:179106600-179108800	Enhancers	Liver	Liver
5	chr5:179106600-179109400	Weak transcription	Left Ventricle	heart
6	chr5:179106600-179109800	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:179106600-179109800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:179106600-179110000	Weak transcription	Fetal Stomach	stomach
9	chr5:179106600-179112600	Weak transcription	Brain Anterior Caudate	brain
10	chr5:179106600-179113600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:179106600-179124200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:179106600-179124800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:179106800-179108600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:179106800-179108600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr5:179106800-179108800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:179106800-179109800	Weak transcription	Lung	lung
17	chr5:179106800-179110200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:179106800-179110600	Weak transcription	Thymus	Thymus
19	chr5:179106800-179123000	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:179107400-179108800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:179107400-179109600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:179107400-179121400	Weak transcription	Primary B cells from cord blood	blood
23	chr5:179107600-179109000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:179107600-179111000	Weak transcription	Stomach Mucosa	stomach
25	chr5:179107600-179117600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:179107600-179119600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:179107600-179123200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:179107600-179123200	Weak transcription	Fetal Thymus	thymus
29	chr5:179107600-179123400	Weak transcription	Fetal Intestine Small	intestine
30	chr5:179107800-179108600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr5:179107800-179108600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr5:179107800-179108600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:179107800-179114400	Weak transcription	Spleen	Spleen
34	chr5:179108000-179108600	Enhancers	Esophagus	oesophagus
35	chr5:179108000-179108600	Enhancers	K562	blood
36	chr5:179108000-179108800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:179108000-179108800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:179108000-179109000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:179108000-179110800	Weak transcription	GM12878-XiMat	blood
40	chr5:179108000-179115600	Weak transcription	Brain Substantia Nigra	brain
41	chr5:179108200-179108600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:179108200-179108800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr5:179108200-179110800	Weak transcription	Pancreas	Pancrea
44	chr5:179108400-179108600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:179108400-179108600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:179108400-179108600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:179108400-179108600	Enhancers	Brain Angular Gyrus	brain
48	chr5:179108400-179108600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr5:179108400-179108800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr5:179108400-179108800	Enhancers	Fetal Kidney	kidney

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