Variant report

Variant	rs2968009
Chromosome Location	chr5:58351607-58351608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10061553	0.80[ASW][hapmap];0.87[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11738454	0.81[CHB][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs11739293	0.87[ASW][hapmap];0.88[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12654005	0.87[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13178315	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs13181587	0.83[ASN][1000 genomes]
rs1353749	0.81[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs1391649	0.88[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16889129	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs28555377	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2910642	0.88[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs929820	0.92[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2968009	C5orf35	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
2	chr5:58336600-58351800	Weak transcription	Fetal Intestine Small	intestine
3	chr5:58336600-58358000	Weak transcription	Fetal Intestine Large	intestine
4	chr5:58336600-58358000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:58337400-58359000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:58338800-58351800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:58338800-58359200	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:58338800-58362000	Weak transcription	Gastric	stomach
9	chr5:58339000-58365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:58340600-58359000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:58343600-58356400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:58346000-58359000	Weak transcription	Stomach Mucosa	stomach
13	chr5:58347200-58353000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:58347200-58359200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:58348200-58362000	Weak transcription	Psoas Muscle	Psoas
16	chr5:58348400-58352200	Weak transcription	Right Ventricle	heart
17	chr5:58348400-58354200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:58349600-58360600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:58350400-58360200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:58350600-58360200	Weak transcription	Fetal Stomach	stomach
21	chr5:58351000-58359000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:58351200-58351800	Enhancers	A549	lung
23	chr5:58351400-58352000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:58351400-58352200	Flanking Active TSS	Hela-S3	cervix
25	chr5:58351600-58352000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:58351600-58352200	Enhancers	HepG2	liver

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