Variant report

Variant	rs1860118
Chromosome Location	chr7:108237706-108237707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10156002	0.82[CEU][hapmap]
rs10270723	0.85[CEU][hapmap]
rs1043615	0.85[CEU][hapmap]
rs17426315	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[YRI][hapmap]
rs2058127	0.82[EUR][1000 genomes];0.82[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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1860118	THAP5	cis	cerebellum	SCAN
rs1860118	DNAJB9	cis	parietal	SCAN
rs1860118	THAP5	cis	lymphoblastoid	seeQTL
rs1860118	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs1860118	DLD	cis	cerebellum	SCAN
rs1860118	RINT1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108233600-108238200	Weak transcription	Brain Germinal Matrix	brain
2	chr7:108233800-108238800	Weak transcription	Fetal Stomach	stomach
3	chr7:108234000-108237800	Weak transcription	Fetal Brain Female	brain
4	chr7:108234000-108238200	Weak transcription	Brain Anterior Caudate	brain
5	chr7:108234200-108238800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:108234200-108238800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:108234200-108239200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:108234400-108238800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr7:108234400-108239000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:108234600-108238000	Weak transcription	Fetal Brain Male	brain
11	chr7:108234800-108238200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:108234800-108244000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:108235200-108239000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:108235400-108238400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:108236800-108238800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:108237600-108238000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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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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