Variant report

Variant	rs2499742
Chromosome Location	chr6:33914260-33914261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33753049..33756842-chr6:33911606..33914460,3	K562	blood:
2	chr6:33913064..33919897-chr6:33920862..33926806,7	K562	blood:
3	chr6:33911755..33914565-chr6:33915931..33918087,3	K562	blood:
4	chr6:33913220..33915544-chr6:33919122..33921053,3	K562	blood:
5	chr6:33896064..33898965-chr6:33913599..33916267,2	MCF-7	breast:
6	chr6:33906140..33909513-chr6:33910845..33914696,4	MCF-7	breast:
7	chr6:33912394..33915055-chr6:33946729..33949481,2	MCF-7	breast:
8	chr6:33906156..33908809-chr6:33914249..33915924,2	MCF-7	breast:
9	chr6:33912597..33914760-chr6:33916307..33917963,2	MCF-7	breast:
10	chr6:33893477..33895597-chr6:33913163..33915930,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2495961	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2495962	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2495968	0.85[ASN][1000 genomes]
rs2499733	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499734	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2499738	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499741	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2499746	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2499747	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499748	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499749	0.82[EUR][1000 genomes]
rs2499751	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2499752	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2499754	0.85[ASN][1000 genomes]
rs7765294	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2499742	HMGA1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33912600-33918800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:33913000-33917800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:33913000-33917800	Weak transcription	Fetal Intestine Large	intestine
4	chr6:33913800-33914800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:33914000-33914600	Bivalent Enhancer	K562	blood
6	chr6:33914000-33915200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:33914200-33915400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:33914200-33915400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:33914200-33918200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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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

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