Variant report

Variant	rs6042118
Chromosome Location	chr20:1397439-1397440
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:1391237..1393735-chr20:1396844..1398411,3	K562	blood:
2	chr20:1396270..1398331-chr20:1415556..1418372,2	K562	blood:
3	chr20:1397101..1400734-chr20:1402092..1406050,4	K562	blood:
4	chr20:1396772..1399275-chr20:1445760..1448572,2	MCF-7	breast:
5	chr20:1304574..1306455-chr20:1396562..1398195,2	MCF-7	breast:
6	chr20:1372637..1374927-chr20:1395955..1398431,2	K562	blood:
7	chr20:1372764..1374884-chr20:1397366..1399828,3	MCF-7	breast:
8	chr20:1396677..1398342-chr20:1402611..1404331,2	MCF-7	breast:
9	chr20:1309378..1311616-chr20:1396285..1399669,3	MCF-7	breast:
10	chr20:1308822..1311082-chr20:1395748..1398133,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000234684	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000088833	Chromatin interaction
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1028508	0.80[ASN][1000 genomes]
rs11087052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs1884388	0.86[ASN][1000 genomes]
rs1884389	0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1884391	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs1998007	0.85[ASN][1000 genomes]
rs2144542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144545	0.87[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2207829	0.85[ASN][1000 genomes]
rs2207830	0.97[ASN][1000 genomes]
rs2317652	0.80[ASN][1000 genomes]
rs3088080	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs3171292	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs3210915	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs36018423	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4352285	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs4546067	0.84[JPT][hapmap]
rs4813133	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs4814229	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814231	0.85[ASN][1000 genomes]
rs4814237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814243	0.85[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs4814244	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs5019244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033691	0.85[ASN][1000 genomes]
rs6033697	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033698	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033707	0.85[ASN][1000 genomes]
rs6033709	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033710	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033726	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033753	0.89[ASN][1000 genomes]
rs6033807	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs6042066	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042071	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042072	0.85[ASN][1000 genomes]
rs6042074	0.85[ASN][1000 genomes]
rs6042088	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042091	0.85[ASN][1000 genomes]
rs6042117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042175	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042197	0.84[ASN][1000 genomes]
rs6042207	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042208	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042209	0.84[ASN][1000 genomes]
rs6042238	0.80[ASN][1000 genomes]
rs6042244	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6042270	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6042283	0.80[ASN][1000 genomes]
rs6042292	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6042354	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6074593	0.85[ASN][1000 genomes]
rs6074623	0.93[ASN][1000 genomes]
rs6079009	0.85[ASN][1000 genomes]
rs6079010	0.85[ASN][1000 genomes]
rs6079012	0.85[ASN][1000 genomes]
rs6079013	0.85[ASN][1000 genomes]
rs6079015	0.85[ASN][1000 genomes]
rs6079133	0.88[JPT][hapmap]
rs6105079	0.85[ASN][1000 genomes]
rs6105081	0.85[ASN][1000 genomes]
rs6105102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105110	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6105165	0.89[JPT][hapmap]
rs6109825	0.85[ASN][1000 genomes]
rs6109893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109894	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131468	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134916	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514382	0.85[ASN][1000 genomes]
rs6514383	0.85[ASN][1000 genomes]
rs6891	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs750424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124053	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs873523	0.84[ASN][1000 genomes]
rs910619	0.87[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs910620	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs926977	0.89[ASN][1000 genomes]
rs932524	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs9575	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS 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	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1817885	chr20:1386940-1400227	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1818242	chr20:1389773-1400227	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1843659	chr20:1389773-1400227	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1843922	chr20:1389773-1400227	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1820441	chr20:1389863-1397898	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6042118	DEFB125	cis	cerebellum	SCAN
rs6042118	NSFL1C	cis	Brain Pons	GTEx
rs6042118	CENPB	cis	cerebellum	SCAN
rs6042118	NSFL1C	cis	multi-tissue	Pritchard
rs6042118	NSFL1C	cis	Temporal Cortex	GTEx
rs6042118	NSFL1C	cis	cerebellum	SCAN
rs6042118	NSFL1C	cis	Frontal Cortex	GTEx
rs6042118	NSFL1C	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1395600-1398000	Weak transcription	Spleen	Spleen
2	chr20:1395600-1399600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:1395600-1399800	Enhancers	NHLF	lung
4	chr20:1395600-1400000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:1395600-1400000	Enhancers	NHDF-Ad	bronchial
6	chr20:1395600-1400200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:1396000-1397600	Enhancers	HMEC	breast
8	chr20:1396000-1398400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:1396200-1399600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:1396400-1398000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr20:1396400-1398400	Enhancers	Hela-S3	cervix
12	chr20:1396400-1399400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr20:1396400-1399600	Enhancers	NH-A	brain
14	chr20:1396400-1400000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:1396400-1400000	Enhancers	Placenta	Placenta
16	chr20:1396400-1400000	Enhancers	HUVEC	blood vessel
17	chr20:1396400-1400000	Enhancers	Osteobl	bone
18	chr20:1396600-1397800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr20:1396600-1398200	Bivalent Enhancer	HepG2	liver
20	chr20:1396600-1399400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr20:1396600-1400000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr20:1396800-1398800	Enhancers	HSMM	muscle
23	chr20:1396800-1400000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr20:1397000-1398000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:1397000-1398000	Flanking Active TSS	NHEK	skin
26	chr20:1397000-1398600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr20:1397000-1399200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr20:1397000-1400000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr20:1397200-1398400	Enhancers	A549	lung
30	chr20:1397200-1399000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:1397400-1397800	Weak transcription	Esophagus	oesophagus

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