Variant report

Variant	rs7087798
Chromosome Location	chr10:96264257-96264258
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10786168	0.83[JPT][hapmap]
rs10882460	0.83[JPT][hapmap]
rs10882463	0.83[JPT][hapmap]
rs10882474	0.83[JPT][hapmap]
rs10882475	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882477	0.83[JPT][hapmap]
rs11187930	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11187939	0.81[JPT][hapmap]
rs11187940	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11187944	0.82[JPT][hapmap]
rs11187952	0.83[JPT][hapmap]
rs11187960	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188009	0.83[JPT][hapmap]
rs11188020	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188036	0.83[EUR][1000 genomes]
rs12221475	0.82[JPT][hapmap]
rs1334595	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1931757	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1977288	0.86[ASW][hapmap];0.96[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1977291	0.86[ASW][hapmap];0.92[CEU][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2031323	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2265366	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2281791	0.83[JPT][hapmap]
rs2764378	0.81[AMR][1000 genomes]
rs3740358	0.83[JPT][hapmap]
rs3781262	0.82[JPT][hapmap]
rs4564258	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs480032	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4918402	0.83[JPT][hapmap]
rs517784	0.83[JPT][hapmap]
rs556055	0.83[JPT][hapmap]
rs6583941	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6583942	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6583947	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs692872	0.83[JPT][hapmap]
rs701885	0.83[JPT][hapmap]
rs7075182	0.84[CEU][hapmap]
rs7078478	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7088008	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7092129	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7096007	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7393240	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7900007	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7913343	0.82[JPT][hapmap]
rs7922956	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7087798	HELLS	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96211600-96292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:96219800-96283400	Weak transcription	Lung	lung
3	chr10:96223200-96293600	Weak transcription	NHDF-Ad	bronchial
4	chr10:96236400-96268600	Weak transcription	HSMMtube	muscle
5	chr10:96237600-96271400	Weak transcription	Placenta	Placenta
6	chr10:96238200-96273400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:96240200-96271000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr10:96244000-96282600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr10:96244400-96283600	Weak transcription	Pancreas	Pancrea
10	chr10:96244400-96304600	Weak transcription	Aorta	Aorta
11	chr10:96245200-96267000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:96247400-96267400	Weak transcription	Fetal Muscle Leg	muscle
13	chr10:96248000-96273800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr10:96249000-96267800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr10:96249200-96267400	Weak transcription	Left Ventricle	heart
16	chr10:96249200-96286200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:96249400-96268600	Weak transcription	Colon Smooth Muscle	Colon
18	chr10:96249400-96288600	Weak transcription	Gastric	stomach
19	chr10:96249600-96267800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:96250400-96281000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr10:96250600-96271400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:96250800-96268600	Weak transcription	Brain Hippocampus Middle	brain
23	chr10:96250800-96281000	Weak transcription	Brain Angular Gyrus	brain
24	chr10:96250800-96294000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr10:96250800-96297400	Weak transcription	Small Intestine	intestine
26	chr10:96251000-96271600	Weak transcription	Brain Substantia Nigra	brain
27	chr10:96251200-96267200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr10:96255600-96267400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:96256000-96267400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:96256000-96267600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:96256000-96268600	Weak transcription	Ovary	ovary
32	chr10:96256200-96271400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:96256200-96283600	Weak transcription	Osteobl	bone
34	chr10:96256400-96271400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:96256800-96271000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr10:96256800-96283800	Weak transcription	Liver	Liver
37	chr10:96257000-96293400	Weak transcription	HepG2	liver
38	chr10:96257200-96271000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:96259200-96266400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr10:96259400-96267400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr10:96259800-96271000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr10:96260200-96266800	Weak transcription	HSMM	muscle
43	chr10:96260400-96267000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:96260400-96267600	Weak transcription	Fetal Lung	lung
45	chr10:96260600-96269400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr10:96261000-96304400	Weak transcription	NH-A	brain
47	chr10:96261800-96268600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr10:96262200-96267600	Weak transcription	Fetal Intestine Large	intestine
49	chr10:96262400-96267400	Weak transcription	Fetal Stomach	stomach
50	chr10:96262600-96267200	Weak transcription	Fetal Muscle Trunk	muscle

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