Variant report

Variant	rs2404983
Chromosome Location	chr1:57048961-57048962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57044467..57046769-chr1:57047569..57049948,2	MCF-7	breast:
2	chr1:57043720..57045227-chr1:57047518..57050298,2	K562	blood:

Variant related genes	Relation type
ENSG00000162407	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1041604	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10789030	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888982	0.82[AMR][1000 genomes]
rs12126955	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1777275	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2065553	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2065555	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2404719	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4469733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588640	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs7545642	0.86[MEX][hapmap]
rs7549799	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv528673	chr1:57048961-57059571	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57045400-57050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:57045400-57051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:57046000-57049000	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:57046000-57050200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:57046000-57050200	Weak transcription	Brain Angular Gyrus	brain
6	chr1:57046000-57050200	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:57046000-57050400	Weak transcription	HSMM	muscle
8	chr1:57046000-57050800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:57046200-57050200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:57046200-57050400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:57046200-57050400	Weak transcription	A549	lung
12	chr1:57046200-57051400	Weak transcription	Osteobl	bone
13	chr1:57046400-57050200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:57047200-57050200	Weak transcription	NHLF	lung
15	chr1:57047400-57050200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:57047600-57050200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:57047600-57050200	Weak transcription	Fetal Lung	lung
18	chr1:57047600-57050200	Weak transcription	HepG2	liver
19	chr1:57047600-57050200	Weak transcription	NHDF-Ad	bronchial
20	chr1:57047600-57050400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:57048000-57050200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:57048000-57050800	Weak transcription	Liver	Liver
23	chr1:57048000-57056000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:57048800-57049200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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