Variant report

Variant	rs57238599
Chromosome Location	chr12:20833916-20833917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12578492	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1399937	0.82[ASN][1000 genomes]
rs1399938	0.88[ASN][1000 genomes]
rs3809208	0.94[ASN][1000 genomes]
rs55661764	0.91[ASN][1000 genomes]
rs57312777	0.94[ASN][1000 genomes]
rs59508686	0.91[ASN][1000 genomes]
rs60480171	0.82[ASN][1000 genomes]
rs61623220	0.82[ASN][1000 genomes]
rs6487131	0.88[ASN][1000 genomes]
rs6487132	0.88[ASN][1000 genomes]
rs67017312	0.94[ASN][1000 genomes]
rs67028347	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72658759	0.82[ASN][1000 genomes]
rs72658760	0.94[ASN][1000 genomes]
rs72658761	0.82[ASN][1000 genomes]
rs7310399	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73240436	0.91[ASN][1000 genomes]
rs73240439	0.85[ASN][1000 genomes]
rs73240441	0.91[ASN][1000 genomes]
rs74065151	0.82[ASN][1000 genomes]
rs7960786	0.82[ASN][1000 genomes]
rs7975280	0.82[ASN][1000 genomes]
rs7975334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978760	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
3	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1054997	chr12:20682009-21292602	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20814600-20834800	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:20816200-20835600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:20816400-20840000	Weak transcription	Right Ventricle	heart
4	chr12:20816800-20834600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:20817000-20834400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:20828200-20838800	Strong transcription	Hela-S3	cervix
7	chr12:20828600-20840200	Weak transcription	Osteobl	bone
8	chr12:20830200-20834000	Weak transcription	A549	lung
9	chr12:20830600-20834600	Strong transcription	Fetal Intestine Large	intestine
10	chr12:20831800-20837600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:20832000-20834200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:20832400-20834200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr12:20832800-20834600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr12:20833000-20834000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:20833000-20834000	Strong transcription	HUVEC	blood vessel
16	chr12:20833000-20834200	Strong transcription	Aorta	Aorta
17	chr12:20833000-20834400	Strong transcription	Duodenum Mucosa	Duodenum
18	chr12:20833000-20834400	Strong transcription	Fetal Kidney	kidney
19	chr12:20833000-20834600	Strong transcription	Fetal Muscle Leg	muscle
20	chr12:20833000-20834600	Strong transcription	Left Ventricle	heart
21	chr12:20833200-20834200	Strong transcription	Ovary	ovary
22	chr12:20833200-20834600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr12:20833200-20840000	Weak transcription	Fetal Intestine Small	intestine
24	chr12:20833400-20834000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:20833400-20834000	Enhancers	Fetal Brain Male	brain
26	chr12:20833400-20834400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:20833400-20834400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr12:20833600-20834400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:20833800-20834200	Enhancers	Brain Anterior Caudate	brain
30	chr12:20833800-20834200	Strong transcription	Fetal Stomach	stomach
31	chr12:20833800-20834400	Enhancers	Brain Substantia Nigra	brain
32	chr12:20833800-20834600	Enhancers	Liver	Liver
33	chr12:20833800-20834600	Enhancers	Brain Hippocampus Middle	brain
34	chr12:20833800-20834600	Enhancers	HepG2	liver
35	chr12:20833800-20836200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:20833800-20839400	Weak transcription	Pancreas	Pancrea

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