Variant report

Variant	rs1399938
Chromosome Location	chr12:20834636-20834637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12578492	0.82[ASN][1000 genomes]
rs12580616	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12580628	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12581970	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1399937	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794270	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809208	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55661764	0.85[ASN][1000 genomes]
rs56174957	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57238599	0.88[ASN][1000 genomes]
rs57312777	0.82[ASN][1000 genomes]
rs59508686	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60480171	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61579575	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61623220	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6487131	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487132	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67017312	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67028347	0.82[ASN][1000 genomes]
rs72658756	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72658759	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72658760	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72658761	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7296571	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7303066	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310399	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7314545	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7316120	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73240436	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73240441	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74065151	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74065172	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74065173	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74066232	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74066238	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74066258	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7956705	1.00[EUR][1000 genomes]
rs7960786	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970439	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7970863	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7971656	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7975280	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975334	0.82[ASN][1000 genomes]
rs7978760	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[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:23 , 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	chr12:20828200-20838800	Strong transcription	Hela-S3	cervix
5	chr12:20828600-20840200	Weak transcription	Osteobl	bone
6	chr12:20831800-20837600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:20833200-20840000	Weak transcription	Fetal Intestine Small	intestine
8	chr12:20833800-20836200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:20833800-20839400	Weak transcription	Pancreas	Pancrea
10	chr12:20834000-20835200	Enhancers	A549	lung
11	chr12:20834000-20836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:20834000-20836200	Weak transcription	HUVEC	blood vessel
13	chr12:20834200-20835800	Weak transcription	Aorta	Aorta
14	chr12:20834200-20835800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:20834200-20842200	Weak transcription	Ovary	ovary
16	chr12:20834200-20846600	Weak transcription	Fetal Stomach	stomach
17	chr12:20834400-20836200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:20834400-20836400	Weak transcription	Fetal Kidney	kidney
19	chr12:20834600-20836200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr12:20834600-20836400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:20834600-20839400	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:20834600-20839600	Weak transcription	Fetal Intestine Large	intestine
23	chr12:20834600-20840600	Weak transcription	Left Ventricle	heart

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