Variant report

Variant	rs346643
Chromosome Location	chr5:135717194-135717195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs173206	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2546662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs346628	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346629	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap]
rs346633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346634	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346636	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346638	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346639	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346642	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346649	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346655	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392598	0.93[ASN][1000 genomes]
rs963590	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs346643	LRRTM2	cis	cerebellum	SCAN
rs346643	CXCL14	cis	parietal	SCAN
rs346643	SKP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:135713600-135720600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:135716600-135717600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
3	chr5:135716600-135717600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
4	chr5:135716800-135717200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr5:135716800-135717200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:135716800-135717400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:135716800-135717600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
8	chr5:135716800-135717600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:135716800-135718600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:135717000-135717200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr5:135717000-135717400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr5:135717000-135718400	Bivalent Enhancer	iPS-15b 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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