Variant report

Variant	rs17397776
Chromosome Location	chr8:102548734-102548735
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:102547230..102548755-chr8:102549652..102551659,2	MCF-7	breast:
2	chr8:102540330..102544194-chr8:102546592..102549049,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253991	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10505010	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10955256	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10955257	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11776316	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11776725	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11783704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12114930	0.88[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13256544	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13263539	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13265291	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17397811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476242	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880634	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1880635	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981361	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2127034	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2127035	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34216075	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs579505	0.82[ASW][hapmap]
rs60028447	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6984360	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs922466	0.92[GIH][hapmap]

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	nsv1024652	chr8:101802121-102587124	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
2	nsv539699	chr8:101802121-102587124	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17397776	DCAF13	cis	parietal	SCAN
rs17397776	FBXO43	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102527000-102551200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr8:102527000-102551400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:102527200-102555400	Weak transcription	Fetal Intestine Small	intestine
4	chr8:102527200-102556800	Weak transcription	Fetal Intestine Large	intestine
5	chr8:102528400-102550600	Weak transcription	Esophagus	oesophagus
6	chr8:102533800-102550200	Weak transcription	HMEC	breast
7	chr8:102533800-102551400	Weak transcription	Pancreas	Pancrea
8	chr8:102536000-102550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:102536800-102550200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr8:102538200-102550400	Weak transcription	Placenta	Placenta
11	chr8:102539200-102550200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr8:102539800-102550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr8:102542400-102550200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:102542600-102549800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:102542600-102550200	Weak transcription	NHEK	skin
16	chr8:102542600-102550400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:102544400-102550200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr8:102544600-102550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr8:102544800-102550200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr8:102545200-102550000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr8:102545200-102550000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr8:102545200-102550200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr8:102545400-102550000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr8:102545400-102550200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr8:102545400-102550200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr8:102546200-102551400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr8:102548400-102551400	Weak transcription	Psoas Muscle	Psoas

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