Variant report

Variant	rs17400505
Chromosome Location	chr2:178573882-178573883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178454525..178456445-chr2:178573217..178575511,2	K562	blood:
2	chr2:178570926..178572812-chr2:178573756..178576490,2	K562	blood:
3	chr2:178573812..178575590-chr2:178578150..178581099,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13421315	0.90[JPT][hapmap]
rs1530035	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3754991	0.83[MEX][hapmap]
rs3754996	0.90[JPT][hapmap]
rs3770044	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3770045	0.90[JPT][hapmap]
rs4893987	0.83[MEX][hapmap]
rs6706739	0.90[JPT][hapmap]
rs7563242	0.90[JPT][hapmap]
rs7605091	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv870023	chr2:178545623-178581407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1005854	chr2:178546907-178586608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2762967	chr2:178546919-178577002	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1005991	chr2:178550049-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1003983	chr2:178551958-178577002	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17400505	TTC30A	cis	parietal	SCAN
rs17400505	FKBP7	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178558200-178576600	Weak transcription	Pancreas	Pancrea
2	chr2:178563000-178574800	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:178573400-178574200	Enhancers	Brain Hippocampus Middle	brain
4	chr2:178573400-178574400	Enhancers	Brain Substantia Nigra	brain
5	chr2:178573600-178574000	Enhancers	Colon Smooth Muscle	Colon
6	chr2:178573600-178574000	Enhancers	Ovary	ovary
7	chr2:178573600-178574200	Enhancers	Brain Angular Gyrus	brain
8	chr2:178573600-178574200	Enhancers	Brain Anterior Caudate	brain
9	chr2:178573600-178574200	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:178573600-178574200	Enhancers	Brain Germinal Matrix	brain
11	chr2:178573600-178574200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr2:178573600-178574200	Enhancers	Fetal Lung	lung
13	chr2:178573600-178574400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:178573600-178574400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:178573600-178574400	Enhancers	Right Atrium	heart
16	chr2:178573600-178574800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:178573600-178575000	Enhancers	Fetal Heart	heart
18	chr2:178573600-178575000	Enhancers	Left Ventricle	heart
19	chr2:178573600-178575600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:178573600-178577600	Enhancers	Fetal Kidney	kidney
21	chr2:178573800-178574200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr2:178573800-178574200	Enhancers	Fetal Muscle Trunk	muscle
23	chr2:178573800-178574400	Enhancers	Right Ventricle	heart

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