Variant report

Variant	rs2296603
Chromosome Location	chr10:90763127-90763128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10887882	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10887883	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12775232	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1324551	0.90[JPT][hapmap]
rs1571011	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1571013	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1800682	0.91[JPT][hapmap]
rs1810763	0.80[EUR][1000 genomes]
rs1926191	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1926192	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1926193	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1926194	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1926195	0.90[JPT][hapmap]
rs1926196	0.91[JPT][hapmap]
rs1977389	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2031610	0.91[CEU][hapmap]
rs2031612	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2147420	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2148286	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2148287	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2182408	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2296600	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296604	0.81[ASN][1000 genomes]
rs2862833	0.81[EUR][1000 genomes]
rs35150762	0.81[EUR][1000 genomes]
rs3740286	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs3752985	0.85[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs3752986	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3781202	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3824730	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs4406737	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4406738	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4934434	0.95[JPT][hapmap]
rs6586160	0.82[CHB][hapmap]
rs6586163	0.91[JPT][hapmap]
rs6586164	0.91[JPT][hapmap]
rs6586165	0.91[JPT][hapmap]
rs6586167	0.91[JPT][hapmap]
rs7069750	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7095466	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7096473	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7097572	0.91[JPT][hapmap]
rs7901656	0.85[ASN][1000 genomes]
rs7910435	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7910825	0.85[JPT][hapmap]
rs7911226	0.81[ASN][1000 genomes]
rs7911752	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs913043	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9658741	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9658742	0.89[ASN][1000 genomes]
rs982764	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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv551841	chr10:90759724-90775756	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2296603	FAS	cis	Muscle Skeletal	GTEx
rs2296603	ACTA2	Cis_1M	lymphoblastoid	RTeQTL
rs2296603	FAS	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90751800-90768200	Weak transcription	Spleen	Spleen
2	chr10:90752000-90770000	Weak transcription	Placenta	Placenta
3	chr10:90752000-90770800	Weak transcription	Esophagus	oesophagus
4	chr10:90752200-90768400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:90752800-90773400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr10:90754000-90779400	Weak transcription	HepG2	liver
7	chr10:90754000-90789600	Weak transcription	A549	lung
8	chr10:90754200-90763200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:90754200-90767000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr10:90755600-90768200	Weak transcription	Lung	lung
11	chr10:90755600-90771400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:90755600-90776000	Weak transcription	Left Ventricle	heart
13	chr10:90755600-90776200	Weak transcription	Pancreas	Pancrea
14	chr10:90756200-90781800	Weak transcription	Stomach Mucosa	stomach
15	chr10:90756800-90769200	Weak transcription	Colonic Mucosa	Colon
16	chr10:90757000-90770800	Weak transcription	Primary B cells from cord blood	blood
17	chr10:90759400-90763600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:90759400-90763800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:90760400-90764800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr10:90760400-90780400	Weak transcription	Brain Angular Gyrus	brain
21	chr10:90760600-90763800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr10:90761600-90763400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr10:90761600-90764000	Enhancers	HUVEC	blood vessel
24	chr10:90761600-90779000	Weak transcription	Dnd41	blood
25	chr10:90761600-90779400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr10:90761800-90763400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr10:90761800-90763400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:90761800-90763600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr10:90761800-90766800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr10:90761800-90767400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:90761800-90767600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr10:90761800-90768000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr10:90761800-90768200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr10:90761800-90768200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr10:90761800-90769000	Weak transcription	NH-A	brain
36	chr10:90761800-90770800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr10:90761800-90773200	Weak transcription	Thymus	Thymus
38	chr10:90761800-90774200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr10:90761800-90776200	Weak transcription	Right Ventricle	heart
40	chr10:90761800-90779600	Weak transcription	HSMMtube	muscle
41	chr10:90761800-90779800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:90761800-90783800	Weak transcription	Gastric	stomach
43	chr10:90761800-90786200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr10:90762000-90767200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr10:90762000-90767400	Weak transcription	Fetal Lung	lung
46	chr10:90762000-90770600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr10:90762000-90775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr10:90762200-90763400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
49	chr10:90762200-90763400	Genic enhancers	NHDF-Ad	bronchial
50	chr10:90762200-90769000	Weak transcription	Stomach Smooth Muscle	stomach

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