Variant report

Variant	rs920559
Chromosome Location	chr4:102218715-102218716
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EMCN-2	chr4:102218141-102219108	NONHSAT097569

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10007902	0.81[JPT][hapmap]
rs1031033	0.95[JPT][hapmap]
rs1031034	0.95[JPT][hapmap]
rs1348161	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1441433	0.93[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes]
rs1530259	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1549513	0.81[JPT][hapmap]
rs1549515	0.83[JPT][hapmap]
rs1549516	0.81[JPT][hapmap]
rs1561719	0.91[EUR][1000 genomes]
rs2028475	0.88[EUR][1000 genomes]
rs2099813	0.91[EUR][1000 genomes]
rs2583389	0.95[JPT][hapmap]
rs2583392	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2583394	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2583395	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2583397	0.85[ASN][1000 genomes]
rs2583398	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2583399	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2583400	0.93[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs2583401	0.93[CEU][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs2583402	0.93[CEU][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2583406	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2583410	0.89[EUR][1000 genomes]
rs2850326	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2850332	0.93[CEU][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2850339	0.89[EUR][1000 genomes]
rs2850344	0.93[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs2850348	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850349	0.91[EUR][1000 genomes]
rs2850350	0.93[CEU][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850351	0.93[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs2850352	0.91[EUR][1000 genomes]
rs2850354	0.91[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850355	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850357	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850358	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850360	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850367	0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2850369	0.86[JPT][hapmap]
rs2850370	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2850371	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2850372	0.85[ASN][1000 genomes]
rs2850954	0.88[EUR][1000 genomes]
rs2850963	0.93[CEU][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2850967	0.89[EUR][1000 genomes]
rs2850969	0.93[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs2850974	0.92[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs2850975	0.92[EUR][1000 genomes]
rs2850976	0.93[CEU][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs4452435	0.81[JPT][hapmap]
rs755961	0.93[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs920560	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs962384	0.89[EUR][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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs920559	AP001816.1	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102207600-102226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:102210200-102225800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:102211200-102219000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:102212200-102220600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:102212200-102226200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:102212600-102227200	Weak transcription	Primary T cells from cord blood	blood
7	chr4:102212800-102221000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:102212800-102227200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:102212800-102228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:102213400-102221000	Weak transcription	Stomach Mucosa	stomach
11	chr4:102214800-102225600	Weak transcription	Brain Anterior Caudate	brain
12	chr4:102214800-102227200	Weak transcription	Gastric	stomach
13	chr4:102214800-102227200	Weak transcription	Psoas Muscle	Psoas
14	chr4:102215000-102227200	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:102215000-102227400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:102215000-102232600	Weak transcription	Pancreas	Pancrea
17	chr4:102215400-102236600	Weak transcription	Primary B cells from cord blood	blood
18	chr4:102216200-102227400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:102217000-102221000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:102218600-102218800	Enhancers	H9 Cell Line	embryonic stem cell
21	chr4:102218600-102218800	Enhancers	Esophagus	oesophagus

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