Variant report

Variant	rs2180421
Chromosome Location	chr1:226160882-226160883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10915916	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2475152	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2749698	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816329	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2816330	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs4653701	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653702	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426091	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426092	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6657197	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6664468	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690247	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2180421	IARS2	cis	cerebellum	SCAN
rs2180421	MOSC1	cis	cerebellum	SCAN
rs2180421	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226129600-226185600	Weak transcription	Right Atrium	heart
2	chr1:226156400-226165400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:226156800-226167200	Weak transcription	HepG2	liver
4	chr1:226156800-226167600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:226157000-226165000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:226157000-226167200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:226157000-226167400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:226157800-226165200	Weak transcription	Spleen	Spleen
9	chr1:226158800-226165400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:226159000-226161000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:226160000-226164600	Weak transcription	Thymus	Thymus
12	chr1:226160200-226162200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:226160400-226161200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:226160400-226161200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:226160800-226161000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:226160800-226161000	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:226160800-226161000	Enhancers	K562	blood
18	chr1:226160800-226163600	Weak transcription	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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