Variant report

Variant	rs17482961
Chromosome Location	chr2:111791077-111791078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:111789979..111793920-chr2:111796275..111799559,5	MCF-7	breast:
2	chr2:111785222..111792269-chr2:111873385..111881089,20	MCF-7	breast:
3	chr2:111777002..111779950-chr2:111790531..111792084,2	MCF-7	breast:
4	chr2:111790430..111792678-chr2:111804599..111806279,2	MCF-7	breast:
5	chr2:111779153..111781716-chr2:111789597..111791988,2	MCF-7	breast:
6	chr2:111790298..111793489-chr2:111807175..111809652,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10167918	0.95[GIH][hapmap];0.82[TSI][hapmap]
rs1038371	0.96[GIH][hapmap]
rs17483466	0.84[ASW][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap]
rs17548346	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849314	0.81[CEU][hapmap]
rs62161543	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6542245	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs752834	0.84[ASW][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap]
rs754352	0.84[ASW][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap]
rs7581900	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7599682	0.96[AMR][1000 genomes];0.93[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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	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
rs17482961	NPHP1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111786000-111795800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:111786200-111792400	Enhancers	Fetal Lung	lung
3	chr2:111786800-111792800	Enhancers	Fetal Intestine Small	intestine
4	chr2:111787000-111792000	Enhancers	Stomach Mucosa	stomach
5	chr2:111787000-111792800	Enhancers	Fetal Intestine Large	intestine
6	chr2:111787400-111795600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:111788000-111791200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:111788000-111791600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:111788200-111791200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:111788200-111792600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:111788200-111793400	Weak transcription	Fetal Thymus	thymus
13	chr2:111788200-111799200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:111788600-111791400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:111789200-111791200	Enhancers	Left Ventricle	heart
16	chr2:111789200-111791200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr2:111789400-111791200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:111789600-111791200	Enhancers	Placenta	Placenta
19	chr2:111790000-111791400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr2:111790200-111791200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:111790200-111791200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:111790200-111791400	Enhancers	Primary B cells from cord blood	blood
23	chr2:111790200-111791400	Enhancers	NHEK	skin
24	chr2:111790200-111791600	Enhancers	HMEC	breast
25	chr2:111790200-111792400	Enhancers	Fetal Heart	heart
26	chr2:111790400-111791200	Enhancers	Gastric	stomach
27	chr2:111790400-111791200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr2:111790800-111791200	Enhancers	A549	lung
29	chr2:111790800-111791200	Enhancers	HepG2	liver
30	chr2:111790800-111791600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr2:111790800-111793600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:111790800-111799200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:111790800-111800200	Weak transcription	Spleen	Spleen
34	chr2:111791000-111791200	Flanking Active TSS	Colonic Mucosa	Colon
35	chr2:111791000-111791200	Flanking Active TSS	Duodenum Mucosa	Duodenum

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