Variant report

Variant	rs1771943
Chromosome Location	chr1:247449996-247449997
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247444095..247447712-chr1:247449743..247453881,5	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10754542	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10924983	0.81[AMR][1000 genomes]
rs10924985	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11578583	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1192830	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1192832	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12035515	0.81[ASN][1000 genomes]
rs1204493	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1341173	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1614597	0.82[CEU][hapmap]
rs1616299	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771929	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1771940	0.81[CEU][hapmap]
rs1771948	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1778544	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1778546	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1778549	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2153631	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2799540	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3850824	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4320815	1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925532	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925533	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925534	0.96[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925615	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs56037169	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56399534	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674425	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6692645	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74163745	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7418221	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7528202	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540329	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552292	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs875883	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9426180	0.95[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9426181	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9426182	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9426233	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9725334	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1771943	ZNF496	cis	lung	GTEx
rs1771943	EDIL3	trans	lymphoblastoid	RTeQTL
rs1771943	ZNF496	cis	Thyroid	GTEx
rs1771943	ZNF496	cis	Nerve Tibial	GTEx
rs1771943	ZNF496	cis	Esophagus Muscularis	GTEx
rs1771943	ZNF496	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247436800-247457000	Weak transcription	HSMMtube	muscle
2	chr1:247445600-247455400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:247449200-247450200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:247449200-247450600	ZNF genes & repeats	Thymus	Thymus
5	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:247449400-247450200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:247449400-247450600	ZNF genes & repeats	Fetal Brain Female	brain
8	chr1:247449400-247451000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:247449600-247450400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:247449600-247450400	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:247449800-247452200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:247449800-247452600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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