Variant report

Variant	rs747533
Chromosome Location	chr10:49756258-49756259
allele	C/T
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	chr10:49756143-49756661	U87	brain:	n/a	n/a
2	POLR2A	chr10:49756143-49756667	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49755429..49757315-chr10:49758822..49761538,2	K562	blood:
2	chr10:49513465..49516141-chr10:49755836..49758473,2	K562	blood:

Variant related genes	Relation type
ENSG00000231906	TF binding region
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10491040	0.81[ASN][1000 genomes]
rs10735226	1.00[JPT][hapmap]
rs10776614	0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10776615	0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10776616	0.88[ASN][1000 genomes]
rs10857592	1.00[JPT][hapmap]
rs10857596	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10857598	0.81[ASN][1000 genomes]
rs11101355	1.00[JPT][hapmap]
rs11101357	1.00[JPT][hapmap]
rs11101368	1.00[JPT][hapmap]
rs11101377	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11101381	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11101382	1.00[JPT][hapmap]
rs11101384	0.90[ASN][1000 genomes]
rs11812546	1.00[JPT][hapmap]
rs12358311	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12358315	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12412164	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12777174	1.00[JPT][hapmap]
rs12777190	1.00[JPT][hapmap]
rs1345104	0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs1345109	0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1345110	0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1345111	0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1348633	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1445148	0.85[ASN][1000 genomes]
rs17697885	1.00[JPT][hapmap]
rs17770615	1.00[JPT][hapmap]
rs1814469	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1838568	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1838569	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1838570	0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1838573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1838574	0.81[ASN][1000 genomes]
rs1838579	0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs1965170	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2077152	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2120910	0.91[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs4080665	1.00[JPT][hapmap]
rs4084916	0.81[ASN][1000 genomes]
rs41510345	1.00[JPT][hapmap]
rs4450130	1.00[JPT][hapmap]
rs4838418	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4838421	0.90[ASN][1000 genomes]
rs4838422	0.90[ASN][1000 genomes]
rs4838605	1.00[JPT][hapmap]
rs4838606	1.00[JPT][hapmap]
rs4838617	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4838623	0.90[ASN][1000 genomes]
rs56058334	0.85[ASN][1000 genomes]
rs6537568	0.84[ASN][1000 genomes]
rs7069220	1.00[JPT][hapmap]
rs7071095	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7071480	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7072237	0.81[ASN][1000 genomes]
rs7074631	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7085183	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7085335	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7087729	1.00[JPT][hapmap]
rs7088010	0.85[ASN][1000 genomes]
rs7093726	1.00[JPT][hapmap]
rs7094216	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7096053	0.86[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7098068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7350424	0.85[ASN][1000 genomes]
rs7350439	0.85[ASN][1000 genomes]
rs7894707	0.92[CHD][hapmap];0.88[GIH][hapmap];0.86[ASN][1000 genomes]
rs7894971	0.90[ASN][1000 genomes]
rs7896644	0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs7904456	0.85[ASN][1000 genomes]
rs7905247	0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs7911247	1.00[JPT][hapmap]
rs7915233	1.00[JPT][hapmap]
rs7916108	0.90[ASN][1000 genomes]
rs935271	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs747533	A1CF	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49734400-49762400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:49735400-49756800	Weak transcription	HSMMtube	muscle
3	chr10:49739400-49762400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
5	chr10:49743800-49757800	Weak transcription	HMEC	breast
6	chr10:49749600-49758800	Weak transcription	NH-A	brain
7	chr10:49751200-49771600	Weak transcription	Pancreas	Pancrea
8	chr10:49751400-49759600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:49752200-49760200	Strong transcription	HSMM	muscle
10	chr10:49753000-49760200	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr10:49753200-49760200	Strong transcription	Osteobl	bone
12	chr10:49753400-49756400	Enhancers	Fetal Stomach	stomach
13	chr10:49753400-49759600	Strong transcription	NHLF	lung
14	chr10:49753400-49764400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:49753800-49759600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:49754000-49757400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr10:49754800-49756600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:49755000-49761800	Weak transcription	Colon Smooth Muscle	Colon
19	chr10:49755200-49756600	Enhancers	Brain Cingulate Gyrus	brain
20	chr10:49755200-49757000	Enhancers	Brain Hippocampus Middle	brain
21	chr10:49755400-49757000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:49755600-49756400	Enhancers	Brain Anterior Caudate	brain
23	chr10:49755600-49756400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr10:49755800-49756800	Enhancers	Brain Substantia Nigra	brain
25	chr10:49755800-49758000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:49756000-49756800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:49756000-49757200	Weak transcription	NHDF-Ad	bronchial
28	chr10:49756000-49757400	Weak transcription	HUVEC	blood vessel
29	chr10:49756000-49760000	Weak transcription	Ovary	ovary
30	chr10:49756200-49757000	Enhancers	Fetal Muscle Trunk	muscle
31	chr10:49756200-49757200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:49756200-49759600	Weak transcription	Brain Angular Gyrus	brain
33	chr10:49756200-49759800	Weak transcription	Fetal Lung	lung

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