Variant report

Variant	rs2499751
Chromosome Location	chr6:33919327-33919328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2495961	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2495962	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2495968	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499733	0.83[ASN][1000 genomes]
rs2499734	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499738	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499741	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499742	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2499746	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2499747	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2499748	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2499749	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2499752	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2499754	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][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	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv462899	chr6:33880480-33944014	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv602841	chr6:33880480-33944014	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2499751	HMGA1	cis	cerebellum	SCAN
rs2499751	TMPRSS3	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33917800-33919600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:33917800-33919600	Enhancers	Fetal Intestine Small	intestine
3	chr6:33917800-33920000	Enhancers	Fetal Intestine Large	intestine
4	chr6:33918000-33919400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:33918200-33919400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:33918200-33919400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr6:33918200-33919600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:33918200-33919600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:33918800-33919600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:33918800-33924400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:33919200-33919600	Bivalent Enhancer	Right Ventricle	heart
12	chr6:33919200-33926200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

Quick Search:

Input of quick search could be:

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

what's new

Quick links