Variant report

Variant	rs17109746
Chromosome Location	chr10:95852129-95852130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1002636	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs10509668	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882382	0.86[CEU][hapmap];0.94[GIH][hapmap]
rs10882386	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882387	0.91[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs10882388	0.91[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs10882389	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10882391	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187768	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs11187773	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11187777	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11187778	0.83[EUR][1000 genomes]
rs11187786	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157003	0.91[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs1157004	0.85[EUR][1000 genomes]
rs12244322	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12254065	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap]
rs12257511	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12266103	0.81[EUR][1000 genomes]
rs12268744	0.90[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs12356494	0.83[EUR][1000 genomes]
rs1343077	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1361810	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418922	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1418923	0.91[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs17109671	0.80[EUR][1000 genomes]
rs17109674	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17109735	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925242	0.91[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1925243	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs1925244	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1925248	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1935962	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs1935963	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998707	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998708	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147738	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147740	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2209442	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3945750	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4145083	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4406757	0.91[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs4567381	0.85[EUR][1000 genomes]
rs4918042	0.91[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs4918043	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4918044	0.91[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs4918045	0.91[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs4918057	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs4918070	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs56406227	0.86[EUR][1000 genomes]
rs56989927	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6583926	0.91[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7075952	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7080228	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7082337	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7082530	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap]
rs7082622	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7082860	0.90[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7084497	0.83[ASW][hapmap];0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7088218	0.85[EUR][1000 genomes]
rs7088723	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7089080	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs7096231	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7096354	0.86[EUR][1000 genomes]
rs7896839	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7910822	0.91[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs7917353	0.91[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs7918106	0.91[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs7922612	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs992632	0.91[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17109746	INPP5K	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95831400-95864200	Weak transcription	Colonic Mucosa	Colon
2	chr10:95836600-95861400	Weak transcription	Pancreas	Pancrea
3	chr10:95836600-95863400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr10:95837600-95876000	Weak transcription	Fetal Intestine Large	intestine
5	chr10:95843400-95864000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr10:95845400-95852600	Weak transcription	HSMMtube	muscle
7	chr10:95845400-95860600	Weak transcription	Spleen	Spleen
8	chr10:95845400-95867800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:95845600-95853400	Weak transcription	Lung	lung
10	chr10:95847800-95860600	Weak transcription	Fetal Intestine Small	intestine
11	chr10:95849000-95852400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr10:95849000-95862200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr10:95849000-95862400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:95849200-95852600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:95849200-95852600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:95849200-95852600	Weak transcription	A549	lung
17	chr10:95849200-95852600	Weak transcription	Osteobl	bone
18	chr10:95849200-95853000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:95849200-95858600	Weak transcription	Fetal Brain Female	brain
20	chr10:95849200-95858600	Weak transcription	Fetal Muscle Leg	muscle
21	chr10:95849200-95863200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr10:95850400-95852800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:95850400-95863400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr10:95850600-95854400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:95850600-95854400	Weak transcription	Left Ventricle	heart
26	chr10:95850600-95858400	Weak transcription	Fetal Lung	lung
27	chr10:95850800-95857400	Weak transcription	Right Atrium	heart
28	chr10:95851000-95852200	Enhancers	Brain Hippocampus Middle	brain
29	chr10:95851200-95852800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr10:95851200-95853000	Weak transcription	Fetal Stomach	stomach
31	chr10:95851200-95853200	Weak transcription	Ovary	ovary
32	chr10:95851200-95853400	Weak transcription	Aorta	Aorta
33	chr10:95851400-95853400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr10:95851400-95857800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:95851600-95854800	Weak transcription	Brain Anterior Caudate	brain
36	chr10:95851800-95853000	Weak transcription	Adipose Nuclei	Adipose
37	chr10:95851800-95854200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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