Variant report

Variant	rs1498609
Chromosome Location	chr5:58344518-58344519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58334717..58336571-chr5:58343611..58346304,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247345	Chromatin interaction
ENSG00000113448	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10514871	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498602	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1498607	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17720311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17776777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17776825	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17777617	0.80[GIH][hapmap]
rs2279737	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55946132	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55970459	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56057207	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62358506	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72770683	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1498609	C5orf35	cis	cerebellum	SCAN
rs1498609	RAB3C	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
2	chr5:58336600-58348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58336600-58351800	Weak transcription	Fetal Intestine Small	intestine
4	chr5:58336600-58358000	Weak transcription	Fetal Intestine Large	intestine
5	chr5:58336600-58358000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:58337400-58359000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:58338200-58347600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:58338400-58350200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:58338800-58351800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:58338800-58359200	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:58338800-58362000	Weak transcription	Gastric	stomach
12	chr5:58339000-58345000	Weak transcription	Fetal Lung	lung
13	chr5:58339000-58351600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:58339000-58365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:58340600-58359000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:58342600-58344800	Enhancers	A549	lung
17	chr5:58343600-58345800	Enhancers	Hela-S3	cervix
18	chr5:58343600-58356400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:58343800-58344800	Weak transcription	Fetal Heart	heart
20	chr5:58344200-58345200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:58344400-58347600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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