Variant report

Variant	rs4814229
Chromosome Location	chr20:1388219-1388220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1388186..1390453-chr20:1399929..1402694,2	K562	blood:
2	chr20:1387186..1389098-chr20:1391471..1393677,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11087052	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13063	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs1884389	0.81[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1884391	0.83[JPT][hapmap]
rs1998007	0.93[ASN][1000 genomes]
rs2144542	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2144543	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2144545	0.85[ASW][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs2207828	0.87[ASN][1000 genomes]
rs2207829	0.93[ASN][1000 genomes]
rs2207830	0.89[ASN][1000 genomes]
rs3088080	0.83[CHD][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs3171292	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs3210915	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs36018423	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4352285	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs4546067	0.84[JPT][hapmap]
rs4813133	0.93[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4814231	0.93[ASN][1000 genomes]
rs4814237	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814240	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814243	0.80[ASN][1000 genomes]
rs4814244	0.86[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs5019244	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033691	0.93[ASN][1000 genomes]
rs6033697	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033698	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033707	0.93[ASN][1000 genomes]
rs6033709	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033715	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033726	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033728	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033729	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033732	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033744	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033753	0.81[ASN][1000 genomes]
rs6033807	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs6042066	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042071	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042072	0.93[ASN][1000 genomes]
rs6042074	0.93[ASN][1000 genomes]
rs6042088	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042091	0.93[ASN][1000 genomes]
rs6042117	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042118	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042131	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042160	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042170	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042172	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042175	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042207	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042208	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042244	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs6042270	0.89[JPT][hapmap];0.82[YRI][hapmap]
rs6042292	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs6042354	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs6074593	0.93[ASN][1000 genomes]
rs6074623	0.85[ASN][1000 genomes]
rs6079009	0.93[ASN][1000 genomes]
rs6079010	0.93[ASN][1000 genomes]
rs6079012	0.93[ASN][1000 genomes]
rs6079013	0.93[ASN][1000 genomes]
rs6079015	0.93[ASN][1000 genomes]
rs6079133	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs6105079	0.93[ASN][1000 genomes]
rs6105081	0.93[ASN][1000 genomes]
rs6105102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6105110	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6105165	0.89[JPT][hapmap];0.86[YRI][hapmap]
rs6109825	0.93[ASN][1000 genomes]
rs6109893	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6109894	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6109912	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6131468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134916	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6514382	0.93[ASN][1000 genomes]
rs6514383	0.93[ASN][1000 genomes]
rs6891	0.83[CHD][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs750424	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8124053	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910619	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs910620	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs926977	0.81[ASN][1000 genomes]
rs932524	0.83[CHD][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs9575	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	esv994443	chr20:1385239-1392933	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	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
5	esv1819763	chr20:1386940-1390683	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv1834375	chr20:1386940-1390683	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	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
8	esv3453894	chr20:1387152-1392750	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv1815191	chr20:1387658-1390682	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	esv1819996	chr20:1387658-1390682	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv1835632	chr20:1387658-1390682	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	esv1841302	chr20:1387658-1390682	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	esv1847243	chr20:1387658-1390682	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	esv1849807	chr20:1387658-1390682	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	esv3497599	chr20:1387952-1391950	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4814229	NSFL1C	cis	cerebellum	SCAN
rs4814229	NSFL1C	cis	Brain Pons	GTEx
rs4814229	NSFL1C	cis	Frontal Cortex	GTEx
rs4814229	NSFL1C	cis	Temporal Cortex	GTEx
rs4814229	SRXN1	cis	cerebellum	SCAN
rs4814229	NSFL1C	cis	brain	seeQTL
rs4814229	DEFB125	cis	cerebellum	SCAN
rs4814229	CENPB	cis	cerebellum	SCAN
rs4814229	NSFL1C	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1380600-1388400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr20:1382400-1388400	Weak transcription	Placenta	Placenta
3	chr20:1383800-1396000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:1384400-1395600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:1384400-1396000	Weak transcription	HMEC	breast

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