Variant report

Variant	rs9472632
Chromosome Location	chr6:45936523-45936524
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs6458479	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6458480	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6458481	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6458482	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6921959	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv428482	chr6:45926644-46050182	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv885867	chr6:45936223-45982976	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9472632	CLIC5	cis	Nerve Tibial	GTEx
rs9472632	CLIC5	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45918800-45938400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:45932600-45937800	Weak transcription	Fetal Intestine Large	intestine
3	chr6:45933600-45941400	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr6:45934400-45937200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:45934400-45937200	Weak transcription	Small Intestine	intestine
6	chr6:45934400-45938600	Enhancers	Right Atrium	heart
7	chr6:45934600-45936800	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr6:45934600-45937600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:45934800-45936800	Weak transcription	Ovary	ovary
10	chr6:45934800-45937400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:45934800-45937600	Weak transcription	Fetal Intestine Small	intestine
12	chr6:45935000-45937600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:45935000-45938400	Weak transcription	Lung	lung
14	chr6:45935200-45936800	Weak transcription	Colonic Mucosa	Colon
15	chr6:45935200-45937800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:45935600-45936800	Weak transcription	Psoas Muscle	Psoas
17	chr6:45935800-45937000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:45935800-45938000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:45936000-45936800	Weak transcription	Left Ventricle	heart
20	chr6:45936000-45937000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:45936000-45941200	Enhancers	Fetal Heart	heart
22	chr6:45936200-45936800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:45936200-45937600	Weak transcription	Right Ventricle	heart
24	chr6:45936400-45936800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:45936400-45936800	Enhancers	Fetal Kidney	kidney
26	chr6:45936400-45936800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr6:45936400-45937000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:45936400-45937600	Active TSS	Rectal Mucosa Donor 29	rectum

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