Variant report

Variant	rs10874521
Chromosome Location	chr1:102312848-102312849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10874524	0.85[EUR][1000 genomes]
rs11164315	1.00[YRI][hapmap]
rs12035099	0.85[EUR][1000 genomes]
rs12062147	1.00[YRI][hapmap]
rs12092384	0.81[CEU][hapmap]
rs12117918	0.84[EUR][1000 genomes]
rs12139929	0.84[EUR][1000 genomes]
rs17125667	0.82[CEU][hapmap]

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	nsv522921	chr1:102170295-102876392	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv522156	chr1:102309649-102421714	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10874521	PALMD	cis	cerebellum	SCAN
rs10874521	DPH5	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:102311000-102313000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:102311200-102313400	Active TSS	Fetal Intestine Large	intestine
3	chr1:102311400-102313400	Active TSS	Fetal Intestine Small	intestine
4	chr1:102312200-102313000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:102312200-102313000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:102312200-102313000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:102312400-102313000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr1:102312400-102313600	Enhancers	Fetal Heart	heart
9	chr1:102312600-102313000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:102312800-102313000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:102312800-102313200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:102312800-102313200	Weak transcription	Fetal Kidney	kidney
13	chr1:102312800-102313400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:102312800-102313600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:102312800-102313600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:102312800-102313600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:102312800-102314200	Weak transcription	Brain Germinal Matrix	brain
18	chr1:102312800-102314800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:102312800-102320400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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

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