Variant report

Variant	rs56004424
Chromosome Location	chr2:173199705-173199706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10182136	0.88[EUR][1000 genomes]
rs55639081	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55998604	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56011402	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs57200533	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57540835	0.87[ASN][1000 genomes]
rs58198619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59279316	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59465816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61071477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61286863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66486916	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6742648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73018804	0.91[EUR][1000 genomes]
rs73018829	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7588553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591203	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7602327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv3034	chr2:173160295-173200113	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173195400-173199800	Weak transcription	Lung	lung
2	chr2:173195400-173199800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:173195400-173204000	Weak transcription	Left Ventricle	heart
4	chr2:173195400-173204000	Weak transcription	Right Ventricle	heart
5	chr2:173197600-173204000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:173197600-173204400	Weak transcription	Thymus	Thymus
7	chr2:173197800-173204000	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:173198000-173199800	Weak transcription	Gastric	stomach
9	chr2:173198000-173200400	Enhancers	HepG2	liver
10	chr2:173198400-173199800	Weak transcription	Fetal Intestine Large	intestine
11	chr2:173198400-173201800	Weak transcription	Small Intestine	intestine
12	chr2:173198400-173204400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:173198600-173199800	Weak transcription	Fetal Intestine Small	intestine
14	chr2:173198600-173199800	Weak transcription	HSMMtube	muscle
15	chr2:173198600-173204000	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:173198600-173204000	Weak transcription	Fetal Thymus	thymus
17	chr2:173198600-173204000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:173198600-173204200	Weak transcription	Fetal Lung	lung
19	chr2:173198800-173200800	Enhancers	Pancreas	Pancrea
20	chr2:173198800-173203600	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:173198800-173204000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:173198800-173204000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:173199000-173203000	Enhancers	Colonic Mucosa	Colon
24	chr2:173199600-173200000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:173199600-173200200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr2:173199600-173200600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr2:173199600-173201800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr2:173199600-173208000	Enhancers	Stomach Mucosa	stomach

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