Variant report

Variant	rs4450130
Chromosome Location	chr10:49733261-49733262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:49732506-49735617	U87	brain:	n/a	n/a
2	POLR2A	chr10:49732512-49735548	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:49732450..49736073-chr10:49745484..49747337,3	K562	blood:
2	chr10:49731096..49734201-chr10:49864172..49866367,3	K562	blood:
3	chr10:49639013..49641362-chr10:49732442..49734428,2	K562	blood:

Variant related genes	Relation type
ARHGAP22	TF binding region
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10491040	0.81[ASN][1000 genomes]
rs10735226	1.00[JPT][hapmap]
rs10776614	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10776615	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10776616	0.82[CHB][hapmap]
rs10857592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857596	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10857598	0.81[ASN][1000 genomes]
rs11101355	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11101357	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11101362	1.00[ASN][1000 genomes]
rs11101364	1.00[ASN][1000 genomes]
rs11101368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101377	1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs11101381	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11101382	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11101384	0.82[CHB][hapmap]
rs11591281	1.00[ASN][1000 genomes]
rs11812546	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs12358311	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12358315	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12412164	0.81[ASN][1000 genomes]
rs12777174	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12777190	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1345104	0.82[CHB][hapmap]
rs1345109	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1345110	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1345111	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1348633	1.00[JPT][hapmap]
rs1445148	0.86[ASN][1000 genomes]
rs1445154	0.97[ASN][1000 genomes]
rs17697885	1.00[JPT][hapmap]
rs17770615	1.00[JPT][hapmap]
rs1814469	1.00[JPT][hapmap]
rs1838568	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1838569	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1838570	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1838573	0.85[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1838574	0.90[ASN][1000 genomes]
rs1838579	0.82[CHB][hapmap]
rs1900021	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1965170	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2077152	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2120910	0.82[CHB][hapmap]
rs34983450	1.00[ASN][1000 genomes]
rs4080665	1.00[JPT][hapmap]
rs4084916	0.81[ASN][1000 genomes]
rs4101278	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41510345	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4838418	1.00[JPT][hapmap]
rs4838605	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4838606	1.00[JPT][hapmap]
rs4838617	0.81[ASN][1000 genomes]
rs4838623	0.82[CHB][hapmap]
rs56058334	0.86[ASN][1000 genomes]
rs56080723	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56248718	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57601353	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60214846	0.80[ASN][1000 genomes]
rs66695288	1.00[ASN][1000 genomes]
rs67372461	1.00[ASN][1000 genomes]
rs7069220	1.00[JPT][hapmap]
rs7071095	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7071480	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7074631	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7085183	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7085335	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7087729	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7088010	0.86[ASN][1000 genomes]
rs7089439	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7093726	1.00[JPT][hapmap]
rs7094216	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7096053	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs7098068	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs72785120	0.93[ASN][1000 genomes]
rs7350424	0.86[ASN][1000 genomes]
rs7350439	0.86[ASN][1000 genomes]
rs747533	1.00[JPT][hapmap]
rs7894707	0.82[CHB][hapmap]
rs7894971	0.82[CHB][hapmap]
rs7896644	0.82[CHB][hapmap]
rs7904456	0.86[ASN][1000 genomes]
rs7905247	0.82[CHB][hapmap]
rs7911247	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7915233	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7916108	0.82[CHB][hapmap]
rs935271	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467191	chr10:49669142-49735563	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv550813	chr10:49669142-49735563	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv550814	chr10:49705142-49735563	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3392447	chr10:49731171-49733719	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4450130	MAPK8	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49731600-49734200	Weak transcription	Fetal Kidney	kidney
2	chr10:49731600-49734200	Weak transcription	Fetal Lung	lung
3	chr10:49731800-49733800	Weak transcription	Brain Substantia Nigra	brain
4	chr10:49732000-49734000	Weak transcription	Colon Smooth Muscle	Colon
5	chr10:49732200-49734000	Weak transcription	HSMMtube	muscle
6	chr10:49732200-49750800	Weak transcription	Gastric	stomach
7	chr10:49732400-49733800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:49732400-49733800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr10:49732400-49734000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:49732400-49734200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr10:49732400-49734200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:49732400-49734200	Weak transcription	Brain Anterior Caudate	brain
13	chr10:49732600-49734000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr10:49732600-49734200	Weak transcription	HMEC	breast
15	chr10:49732600-49735200	Weak transcription	Pancreas	Pancrea
16	chr10:49732800-49733400	Genic enhancers	HSMM	muscle
17	chr10:49732800-49733800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:49732800-49733800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:49732800-49733800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:49732800-49733800	Weak transcription	NH-A	brain
21	chr10:49732800-49734000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:49732800-49734000	Genic enhancers	Muscle Satellite Cultured Cells	--
23	chr10:49732800-49734000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:49732800-49734000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr10:49732800-49734000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr10:49732800-49734000	Weak transcription	Ovary	ovary
27	chr10:49732800-49734000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:49732800-49734000	Enhancers	NHDF-Ad	bronchial
29	chr10:49732800-49734000	Enhancers	Osteobl	bone
30	chr10:49732800-49734200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:49732800-49734200	Weak transcription	Brain Angular Gyrus	brain
32	chr10:49732800-49734200	Weak transcription	Brain Hippocampus Middle	brain
33	chr10:49732800-49734200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:49732800-49734400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr10:49732800-49735000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr10:49732800-49736200	Enhancers	HUVEC	blood vessel
37	chr10:49732800-49736800	Weak transcription	Right Atrium	heart
38	chr10:49732800-49742000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr10:49733000-49734000	Weak transcription	K562	blood
40	chr10:49733200-49733400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:49733200-49733600	Weak transcription	NHLF	lung
42	chr10:49733200-49734000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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