Variant report

Variant	rs7779854
Chromosome Location	chr7:102551582-102551583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10487281	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10487284	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11496066	1.00[CHB][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs12113073	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12113759	1.00[CHB][hapmap]
rs17135875	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17135913	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135916	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474893	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2041094	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2228687	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2411061	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs3893651	1.00[ASN][1000 genomes]
rs4377880	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4398822	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4610658	1.00[CHB][hapmap]
rs55681588	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781834	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849741	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55851590	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56314487	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336567	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56692051	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465886	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs66712128	0.88[EUR][1000 genomes]
rs6955064	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964296	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968036	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727175	1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs73192015	1.00[ASN][1000 genomes]
rs73192019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192025	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73192026	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73714541	0.88[EUR][1000 genomes]
rs7781557	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7798582	0.88[EUR][1000 genomes]
rs7809047	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7779854	LRRC17	cis	Stomach	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:102538400-102553200	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:102539200-102551800	Weak transcription	Fetal Lung	lung
4	chr7:102539200-102553000	Weak transcription	Right Atrium	heart
5	chr7:102547000-102552200	Weak transcription	Stomach Mucosa	stomach
6	chr7:102547200-102554800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:102548200-102558000	Weak transcription	Pancreas	Pancrea
8	chr7:102549000-102551600	ZNF genes & repeats	K562	blood
9	chr7:102549200-102553200	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:102549400-102552600	Weak transcription	HUVEC	blood vessel
11	chr7:102549400-102553400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:102549800-102553000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:102549800-102553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:102550400-102552200	Weak transcription	HSMM	muscle
15	chr7:102550600-102553200	Weak transcription	Fetal Intestine Small	intestine
16	chr7:102550600-102553400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:102550800-102552800	Weak transcription	Fetal Stomach	stomach
18	chr7:102551000-102553200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:102551000-102553600	Weak transcription	Gastric	stomach
20	chr7:102551400-102553200	Weak transcription	Left Ventricle	heart

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