Variant report

Variant	rs17235684
Chromosome Location	chr3:56594121-56594122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11130526	0.88[CEU][hapmap]
rs17235662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17235684	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56591800-56596000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:56591800-56599800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:56592400-56594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:56592400-56594600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:56592400-56594800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:56592400-56594800	Weak transcription	HSMM	muscle
9	chr3:56592400-56596000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:56592400-56596000	Weak transcription	Fetal Stomach	stomach
11	chr3:56592400-56596800	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:56592400-56599800	Weak transcription	Fetal Lung	lung
13	chr3:56592400-56600000	Weak transcription	Ovary	ovary
14	chr3:56592400-56601200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:56592400-56601400	Weak transcription	Left Ventricle	heart
16	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:56592400-56601800	Weak transcription	Lung	lung
18	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
20	chr3:56592400-56602800	Weak transcription	Gastric	stomach
21	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
22	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
23	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
24	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
26	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
27	chr3:56592600-56594200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:56592600-56594200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:56592600-56594200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr3:56592600-56594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:56592600-56594200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:56592600-56594400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:56592600-56594600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:56592600-56594600	Weak transcription	Osteobl	bone
35	chr3:56592600-56594800	Weak transcription	Liver	Liver
36	chr3:56592600-56594800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:56592600-56595600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:56592600-56595800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:56592600-56596000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:56592600-56596000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:56592600-56598600	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:56592600-56598800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:56592600-56599600	Weak transcription	Thymus	Thymus
44	chr3:56592600-56600000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:56592600-56600000	Weak transcription	Colonic Mucosa	Colon
46	chr3:56592600-56600200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:56592600-56600200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:56592600-56600200	Weak transcription	NHLF	lung
49	chr3:56592600-56601000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:56592600-56601000	Weak transcription	HSMMtube	muscle

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