Variant report

Variant	rs12203677
Chromosome Location	chr6:53832566-53832567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10948782	0.81[CEU][hapmap]
rs12192118	0.84[CEU][hapmap]
rs12195491	0.84[CEU][hapmap]
rs12201094	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12203793	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207906	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211770	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1325826	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4639324	0.81[CEU][hapmap]
rs6909547	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6910097	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72951460	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772843	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12203677	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53827400-53836000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:53827400-53836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:53827800-53836000	Weak transcription	Psoas Muscle	Psoas
4	chr6:53832000-53832600	Enhancers	H9 Cell Line	embryonic stem cell
5	chr6:53832000-53832600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:53832000-53832600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:53832000-53832800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr6:53832000-53833400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:53832200-53832600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:53832200-53832600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:53832200-53832800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:53832200-53833200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr6:53832200-53834400	Enhancers	Dnd41	blood

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

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