Variant report

Variant	rs483143
Chromosome Location	chr6:27846744-27846745
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	chr6:27111904..27114162-chr6:27845915..27848477,2	K562	blood:

Extended variants
information (count: 122 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1010261	0.88[CHB][hapmap]
rs1015075	0.85[JPT][hapmap]
rs13194781	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs13195728	0.85[EUR][1000 genomes]
rs13199649	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs13199772	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs13199906	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs13200214	0.91[CEU][hapmap]
rs13212318	0.91[CEU][hapmap]
rs13212651	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs13215275	0.91[CEU][hapmap]
rs13216117	0.85[EUR][1000 genomes]
rs13217620	0.91[CEU][hapmap]
rs13218875	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs149943	0.91[CEU][hapmap]
rs149990	0.91[CEU][hapmap]
rs16867962	1.00[CHB][hapmap]
rs169287	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs175597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17693877	1.00[CHB][hapmap]
rs17693963	0.91[CEU][hapmap]
rs17695758	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs17750747	0.91[CEU][hapmap]
rs17751184	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs17763089	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs183225	1.00[JPT][hapmap]
rs188015	0.83[EUR][1000 genomes]
rs200466	1.00[JPT][hapmap]
rs200469	1.00[JPT][hapmap]
rs200473	1.00[JPT][hapmap]
rs200479	1.00[JPT][hapmap]
rs200481	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs200482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs200483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs200484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs200485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs200488	0.84[ASN][1000 genomes]
rs200489	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs200493	0.90[EUR][1000 genomes]
rs200497	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs200948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200950	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200952	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200964	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs200965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs200966	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs200968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs200973	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs200974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs200975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs200976	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs200977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200979	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs200980	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs200981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs200983	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200992	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200996	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs201002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs202906	0.90[CEU][hapmap]
rs2277104	0.82[ASN][1000 genomes]
rs2747054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28360499	0.83[EUR][1000 genomes]
rs34194357	0.88[EUR][1000 genomes]
rs34295134	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34706883	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs34718920	0.85[EUR][1000 genomes]
rs34788973	0.85[EUR][1000 genomes]
rs35819751	0.88[EUR][1000 genomes]
rs36101351	0.85[EUR][1000 genomes]
rs36108923	0.84[ASN][1000 genomes]
rs36116761	0.88[EUR][1000 genomes]
rs370155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs390764	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs401754	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs401763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs425335	0.91[CEU][hapmap]
rs45509595	0.88[EUR][1000 genomes]
rs4713122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4713127	0.91[ASN][1000 genomes]
rs493161	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs494887	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs557042	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56870390	0.84[ASN][1000 genomes]
rs61742093	0.85[EUR][1000 genomes]
rs666846	1.00[JPT][hapmap]
rs66868086	0.88[EUR][1000 genomes]
rs67040724	0.85[EUR][1000 genomes]
rs67101035	0.85[EUR][1000 genomes]
rs71559050	0.85[EUR][1000 genomes]
rs71559054	0.85[EUR][1000 genomes]
rs904142	0.85[JPT][hapmap]
rs9348779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9357052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9368531	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9368534	0.82[ASN][1000 genomes]
rs9368535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9368536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9368537	0.85[JPT][hapmap]
rs9380018	0.80[ASN][1000 genomes]
rs9380026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9380028	0.85[JPT][hapmap]
rs9380030	0.85[JPT][hapmap]
rs9393845	0.88[CHB][hapmap]
rs9393854	1.00[CHB][hapmap]
rs9393858	0.82[ASN][1000 genomes]
rs9393862	0.91[ASN][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
7	nsv965700	chr6:27845514-27848765	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs483143	AL022393.7	cis	Muscle Skeletal	GTEx
rs483143	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs483143	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs483143	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27841800-27847000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:27842200-27857000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:27842400-27847400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:27842400-27850600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:27842600-27855600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:27842800-27855600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:27843200-27849200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:27844200-27847200	Weak transcription	Dnd41	blood
9	chr6:27844400-27847200	Weak transcription	Fetal Thymus	thymus

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