Variant report

Variant	rs1156380
Chromosome Location	chr6:53862396-53862397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC1-1	chr6:53859762-53862465	ENSG00000236740.2

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1022929	0.87[AMR][1000 genomes]
rs1022930	0.87[AMR][1000 genomes]
rs1022931	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs10484651	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs10484652	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs10484653	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs10948793	0.82[ASN][1000 genomes]
rs10948795	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs1156379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961988	0.91[CEU][hapmap];0.87[AMR][1000 genomes]
rs12194304	0.88[CEU][hapmap];0.88[AMR][1000 genomes]
rs12195852	0.84[AMR][1000 genomes]
rs12199925	0.87[AMR][1000 genomes]
rs12201302	0.88[CEU][hapmap];0.88[AMR][1000 genomes]
rs12524379	0.88[AMR][1000 genomes]
rs1325821	0.80[JPT][hapmap]
rs1570911	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs1570912	0.82[CEU][hapmap];0.87[AMR][1000 genomes]
rs16884583	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs2397153	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs4712052	0.87[AMR][1000 genomes]
rs4715435	0.91[CEU][hapmap];0.87[AMR][1000 genomes]
rs62397360	0.88[AMR][1000 genomes]
rs927795	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349691	0.81[JPT][hapmap]
rs9349692	0.81[JPT][hapmap]
rs9357783	0.81[JPT][hapmap]
rs9395896	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
4	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1018062	chr6:53842588-53925192	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv515808	chr6:53855489-53865667	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2763552	chr6:53856580-53864523	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53852400-53867800	Weak transcription	Fetal Heart	heart
2	chr6:53861000-53862600	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr6:53861000-53867200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:53861200-53863400	Weak transcription	NHEK	skin
5	chr6:53861200-53863800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:53861200-53866200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:53861200-53866400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:53861400-53862800	Weak transcription	Liver	Liver
9	chr6:53862000-53870000	Weak transcription	Aorta	Aorta
10	chr6:53862200-53865600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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