Variant report

Variant	rs12024779
Chromosome Location	chr1:209887212-209887213
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	chr1:209877047..209878564-chr1:209885238..209887392,2	K562	blood:

Variant related genes	Relation type
ENSG00000117594	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11119333	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799643	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12040780	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12075595	1.00[EUR][1000 genomes]
rs17015053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015095	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015099	1.00[EUR][1000 genomes]
rs56679555	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56822893	0.95[AFR][1000 genomes]
rs57606822	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58627173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61279558	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680324	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1004343	chr1:209879304-209909385	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv525445	chr1:209885318-209912593	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209878600-209888200	Weak transcription	Brain Angular Gyrus	brain
2	chr1:209878800-209893400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:209883000-209887400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:209884000-209889000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:209884400-209887400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:209885000-209888200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:209886000-209887400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:209886400-209887400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:209886400-209893200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:209886400-209896400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:209886600-209888000	Weak transcription	NHEK	skin
12	chr1:209886600-209889000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:209886600-209889000	Strong transcription	Liver	Liver
14	chr1:209886800-209888400	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:209887000-209889000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:209887000-209889000	Enhancers	Brain Hippocampus Middle	brain
17	chr1:209887000-209889000	Enhancers	Brain Substantia Nigra	brain
18	chr1:209887200-209887400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:209887200-209887600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:209887200-209888200	Enhancers	HMEC	breast

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