Variant report

Variant	rs12142944
Chromosome Location	chr1:84380880-84380881
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	SETDB1	chr1:84380755-84380924	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
TTLL7	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10489508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10493742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10493743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs11163863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11163864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12116464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12116522	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12116857	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12118371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12118428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[EUR][1000 genomes]
rs12119338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12119424	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12119854	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12120801	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12120905	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12121058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12121629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12123323	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12125111	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12125251	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12126397	1.00[EUR][1000 genomes]
rs12126515	0.96[EUR][1000 genomes]
rs12127526	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12127657	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12128942	0.92[AMR][1000 genomes]
rs12129276	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12131968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12133196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12133949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12135679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12136835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12138857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12140562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs12140964	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12141004	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12141166	1.00[EUR][1000 genomes]
rs12142873	0.92[EUR][1000 genomes]
rs12143951	1.00[CHB][hapmap]
rs12144066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12144704	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12145472	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1408474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1408475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17130437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17130475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17475494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17534879	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1925712	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2031371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2147394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2181901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2389650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41293003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41293005	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4258240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4387198	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs45515591	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56159052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6700983	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7519127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs9645391	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9645396	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9645397	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871551	chr1:84354464-84453223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84333400-84382400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:84345600-84384400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:84346800-84382400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:84351000-84391400	Weak transcription	Fetal Stomach	stomach
5	chr1:84352800-84382400	Weak transcription	Brain Anterior Caudate	brain
6	chr1:84355800-84382200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:84355800-84382600	Weak transcription	Adipose Nuclei	Adipose
8	chr1:84360600-84384600	Weak transcription	Aorta	Aorta
9	chr1:84362600-84403200	Weak transcription	Fetal Brain Male	brain
10	chr1:84366200-84384600	Weak transcription	Gastric	stomach
11	chr1:84366400-84392800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:84366600-84382200	Weak transcription	Fetal Brain Female	brain
13	chr1:84366800-84399400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:84367800-84385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:84368000-84390000	Weak transcription	NH-A	brain
16	chr1:84368000-84394200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:84368200-84384400	Weak transcription	HMEC	breast
18	chr1:84368200-84393400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:84368200-84393800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:84368200-84394800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:84368400-84416600	Weak transcription	NHLF	lung
22	chr1:84368400-84428400	Weak transcription	Pancreas	Pancrea
23	chr1:84368600-84382400	Weak transcription	NHDF-Ad	bronchial
24	chr1:84373400-84383000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:84374200-84393000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:84376200-84392800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:84376400-84382400	Weak transcription	HSMM	muscle
28	chr1:84376800-84382400	Weak transcription	Brain Angular Gyrus	brain
29	chr1:84376800-84405000	Weak transcription	Left Ventricle	heart
30	chr1:84378600-84390200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:84378800-84382200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:84378800-84382400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:84379200-84386000	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:84379800-84382400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:84380200-84381000	Strong transcription	Brain Hippocampus Middle	brain
36	chr1:84380200-84382600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:84380400-84381000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:84380400-84381000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
39	chr1:84380400-84381000	Strong transcription	Brain Substantia Nigra	brain
40	chr1:84380400-84381000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:84380400-84381200	Strong transcription	Brain Germinal Matrix	brain
42	chr1:84380800-84382400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:84380800-84382400	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:84380800-84382400	Weak transcription	HSMMtube	muscle
45	chr1:84380800-84382600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:84380800-84387800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:84380800-84392200	Weak transcription	NHEK	skin

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