Variant report

Variant	rs17335566
Chromosome Location	chr3:99974472-99974473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99973186..99976114-chr3:99977290..99980794,4	K562	blood:
2	chr3:99968089..99970070-chr3:99974045..99975885,2	K562	blood:
3	chr3:99972497..99974715-chr6:139307981..139310479,2	MCF-7	breast:
4	chr3:99971442..99977426-chr3:99977772..99982553,8	MCF-7	breast:
5	chr3:99973186..99975181-chr3:99976513..99979207,3	K562	blood:

Variant related genes	Relation type
ENSG00000036054	Chromatin interaction
ENSG00000135597	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1060452	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11918291	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11920015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11924911	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486660	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486865	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12490043	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12490140	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492610	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12493917	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17335614	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171205	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277657	0.88[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs4928116	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928117	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928120	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs4928161	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4928166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928170	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55950446	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56181320	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56311459	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57271189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62281663	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17335566	C3orf26	cis	multi-tissue	Pritchard
rs17335566	TBC1D23	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99964600-99978600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:99964800-99979000	Weak transcription	Aorta	Aorta
3	chr3:99965200-99978800	Weak transcription	NH-A	brain
4	chr3:99965600-99978800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:99966600-99979000	Weak transcription	Gastric	stomach
6	chr3:99968000-99978800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:99972200-99975200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:99972600-99975400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:99972800-99975200	Weak transcription	NHDF-Ad	bronchial
10	chr3:99972800-99976200	Weak transcription	K562	blood
11	chr3:99973000-99975200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:99973000-99975400	Weak transcription	NHLF	lung
13	chr3:99973000-99978800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:99973200-99975000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:99973400-99975200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:99973400-99975400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:99973400-99975400	Weak transcription	Osteobl	bone
18	chr3:99973400-99976200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:99973400-99978400	Weak transcription	Fetal Stomach	stomach
20	chr3:99973400-99978800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:99973400-99978800	Weak transcription	Fetal Intestine Large	intestine
22	chr3:99973400-99979000	Weak transcription	Fetal Intestine Small	intestine
23	chr3:99973400-99979000	Weak transcription	Left Ventricle	heart
24	chr3:99973400-99979000	Weak transcription	HSMM	muscle
25	chr3:99973600-99975400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:99973600-99976200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:99973600-99976600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:99973600-99978200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:99973600-99978800	Weak transcription	HSMMtube	muscle
30	chr3:99973800-99978800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:99974000-99976200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:99974000-99978400	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:99974200-99975400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:99974200-99977000	Enhancers	HepG2	liver

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