Variant report

Variant	rs2004665
Chromosome Location	chr10:49762077-49762078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49761230..49763552-chr10:49773026..49775938,2	K562	blood:
2	chr10:49760107..49762474-chr10:49763848..49765679,2	K562	blood:

Variant related genes	Relation type
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1078261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11101383	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598598	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs11599380	1.00[CHD][hapmap]
rs12766573	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1373793	1.00[CHD][hapmap]
rs1373795	1.00[CHB][hapmap]
rs1838571	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs1838572	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867588	1.00[CHD][hapmap]
rs4838419	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838619	0.80[EUR][1000 genomes]
rs4838620	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537567	0.81[GIH][hapmap]
rs7093632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs747532	0.84[CEU][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs7895981	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7911418	0.91[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7919520	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs935265	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935266	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935267	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs935268	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs935269	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs935270	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs935276	1.00[JPT][hapmap]

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
rs2004665	A1CF	cis	cerebellum	SCAN

Chromatin state (count:37 , 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	chr10:49739400-49762400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
4	chr10:49751200-49771600	Weak transcription	Pancreas	Pancrea
5	chr10:49753400-49764400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:49757400-49782200	Weak transcription	HSMMtube	muscle
7	chr10:49758200-49762400	Weak transcription	Right Atrium	heart
8	chr10:49758400-49762200	Weak transcription	HMEC	breast
9	chr10:49759200-49770400	Weak transcription	NH-A	brain
10	chr10:49759400-49763800	Enhancers	Brain Substantia Nigra	brain
11	chr10:49759800-49763600	Enhancers	Brain Cingulate Gyrus	brain
12	chr10:49759800-49764200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr10:49760200-49764600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr10:49760400-49762200	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:49760600-49762200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr10:49760600-49762400	Weak transcription	Right Ventricle	heart
17	chr10:49760800-49762200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:49760800-49762200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:49760800-49762400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:49760800-49765000	Strong transcription	NHLF	lung
21	chr10:49760800-49765400	Strong transcription	HSMM	muscle
22	chr10:49760800-49765600	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr10:49760800-49768800	Weak transcription	Ovary	ovary
24	chr10:49761000-49764800	Strong transcription	Osteobl	bone
25	chr10:49761000-49765400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:49761400-49762800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr10:49761400-49764400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:49761400-49765600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:49761600-49780600	Weak transcription	HUVEC	blood vessel
30	chr10:49761800-49762800	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:49761800-49763600	Enhancers	Colon Smooth Muscle	Colon
32	chr10:49761800-49765400	Strong transcription	NHDF-Ad	bronchial
33	chr10:49762000-49762600	Enhancers	Brain Angular Gyrus	brain
34	chr10:49762000-49763600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:49762000-49764400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:49762000-49764600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:49762000-49765600	Weak transcription	H1 Cell Line	embryonic stem cell

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