Variant report

Variant	rs6703684
Chromosome Location	chr1:94300963-94300964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10874797	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164970	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164973	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164974	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11582870	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12097812	0.81[EUR][1000 genomes]
rs1884019	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2092700	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143991	0.80[ASN][1000 genomes]
rs2391315	0.82[EUR][1000 genomes]
rs2747036	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2747037	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2747038	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2747040	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2747042	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747044	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747047	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747049	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2818161	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2818165	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2818166	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2818167	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4520428	0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4847184	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4847192	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847254	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4847257	0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6541399	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660210	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523787	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7526082	0.85[ASN][1000 genomes]
rs7552293	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947343	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases
3	esv1831177	chr1:94288524-94304239	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6703684	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs6703684	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs6703684	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6703684	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs6703684	RP11-488P3.1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94279600-94302800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:94283400-94310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:94284200-94306200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:94284200-94311200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:94290200-94311400	Weak transcription	Aorta	Aorta
6	chr1:94292600-94303200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:94294000-94302200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:94294200-94305400	Weak transcription	A549	lung
9	chr1:94295400-94310000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:94296200-94302000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
11	chr1:94298200-94307000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:94298800-94305000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:94299000-94308600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:94299400-94310200	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:94300600-94309400	Weak transcription	Dnd41	blood
16	chr1:94300800-94311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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