Variant report

Variant	rs10852738
Chromosome Location	chr17:66486827-66486828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:66480053..66482691-chr17:66486689..66489527,2	K562	blood:
2	chr17:66486129..66489864-chr17:66505965..66510014,4	MCF-7	breast:
3	chr17:66486234..66488484-chr17:66491556..66493277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10491176	1.00[CEU][hapmap]
rs16972996	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap]
rs16973034	1.00[CEU][hapmap]
rs2015212	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap]
rs2302235	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap]
rs3785905	1.00[CEU][hapmap];0.85[CHD][hapmap];0.81[YRI][hapmap]
rs56112060	0.85[EUR][1000 genomes]
rs57936225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72847781	0.82[EUR][1000 genomes]
rs8067357	0.85[EUR][1000 genomes]
rs8082254	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[MEX][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	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
2	esv3419888	chr17:66484382-66486930	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10852738	WIPI1	cis	multi-tissue	Pritchard
rs10852738	WIPI1	cis	parietal	SCAN
rs10852738	PITPNC1	cis	cerebellum	SCAN
rs10852738	INTS2	cis	cerebellum	SCAN
rs10852738	WIPI1	cis	cerebellum	SCAN
rs10852738	ABCA10	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66467800-66487000	Weak transcription	Right Atrium	heart
2	chr17:66478400-66487600	Weak transcription	Gastric	stomach
3	chr17:66480800-66490600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr17:66481400-66488200	Weak transcription	Brain Hippocampus Middle	brain
5	chr17:66481600-66487000	Weak transcription	Brain Substantia Nigra	brain
6	chr17:66482000-66487000	Weak transcription	Placenta	Placenta
7	chr17:66482400-66487000	Weak transcription	Ovary	ovary
8	chr17:66482600-66487800	Weak transcription	Liver	Liver
9	chr17:66483000-66487000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr17:66484400-66487600	Weak transcription	Esophagus	oesophagus
11	chr17:66484600-66487600	Weak transcription	HepG2	liver
12	chr17:66484800-66487000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr17:66485000-66487800	Weak transcription	Fetal Thymus	thymus
14	chr17:66485600-66488200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:66486000-66488000	Enhancers	Adipose Nuclei	Adipose
16	chr17:66486000-66488200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:66486000-66488200	Enhancers	Primary B cells from peripheral blood	blood
18	chr17:66486200-66487200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr17:66486200-66487200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:66486200-66488200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:66486200-66488200	Enhancers	Psoas Muscle	Psoas
22	chr17:66486200-66488400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr17:66486200-66488600	Enhancers	GM12878-XiMat	blood
24	chr17:66486200-66488800	Enhancers	Primary B cells from cord blood	blood
25	chr17:66486200-66488800	Enhancers	Fetal Muscle Leg	muscle
26	chr17:66486200-66488800	Enhancers	Lung	lung
27	chr17:66486400-66487600	Weak transcription	Fetal Lung	lung
28	chr17:66486400-66487600	Weak transcription	Pancreas	Pancrea
29	chr17:66486400-66488000	Enhancers	Colonic Mucosa	Colon
30	chr17:66486400-66488600	Enhancers	Spleen	Spleen
31	chr17:66486400-66488800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr17:66486400-66488800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr17:66486600-66487600	Weak transcription	Left Ventricle	heart
34	chr17:66486800-66487400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr17:66486800-66488000	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr17:66486800-66488200	Enhancers	Primary hematopoietic stem cells	blood
37	chr17:66486800-66488600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links