Variant report

Variant	rs6429561
Chromosome Location	chr1:45762934-45762935
allele	G/T
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	chr1:45476319..45479273-chr1:45762744..45765021,2	MCF-7	breast:
2	chr1:45747656..45749487-chr1:45762522..45765596,3	K562	blood:
3	chr1:45761163..45763441-chr1:45763531..45765423,2	K562	blood:
4	chr1:45476357..45485239-chr1:45761850..45773601,48	K562	blood:
5	chr1:45747190..45749487-chr1:45762522..45764661,3	K562	blood:
6	chr1:45761540..45764503-chr1:45766248..45768946,2	K562	blood:
7	chr1:45761109..45763795-chr1:45769192..45770940,3	K562	blood:
8	chr1:45284741..45287398-chr1:45762792..45766811,5	K562	blood:
9	chr1:45761061..45765465-chr1:45766442..45769712,4	MCF-7	breast:
10	chr1:45476265..45486633-chr1:45761064..45774272,63	K562	blood:

No data

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1144868	0.81[JPT][hapmap]
rs1226747	0.81[JPT][hapmap]
rs13374935	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1938296	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1938301	0.81[JPT][hapmap]
rs2105458	0.81[JPT][hapmap]
rs2186219	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2356302	0.81[JPT][hapmap]
rs2997461	0.81[JPT][hapmap]
rs2997465	0.81[JPT][hapmap]
rs3009969	0.81[JPT][hapmap]
rs3009974	0.80[JPT][hapmap]
rs3009979	0.81[JPT][hapmap]
rs3121732	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3121736	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3128438	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3128439	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3128440	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34134455	0.81[JPT][hapmap]
rs346693	0.81[JPT][hapmap]
rs346696	0.81[JPT][hapmap]
rs346717	0.81[JPT][hapmap]
rs346719	0.81[JPT][hapmap]
rs346724	0.81[JPT][hapmap]
rs346732	0.81[JPT][hapmap]
rs346733	0.81[JPT][hapmap]
rs346736	0.81[JPT][hapmap]
rs365108	0.81[JPT][hapmap]
rs3850856	0.81[JPT][hapmap]
rs4233496	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233497	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376776	0.94[ASN][1000 genomes]
rs4376777	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs454624	0.81[JPT][hapmap]
rs4603171	0.92[ASN][1000 genomes]
rs4660839	0.89[JPT][hapmap]
rs4660841	0.81[JPT][hapmap]
rs4660842	0.81[JPT][hapmap]
rs58579477	0.97[ASN][1000 genomes]
rs60115828	0.97[ASN][1000 genomes]
rs61789823	0.92[ASN][1000 genomes]
rs61789838	0.97[ASN][1000 genomes]
rs61789841	1.00[ASN][1000 genomes]
rs6429562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72686440	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv3406025	chr1:45739908-45763848	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45757800-45763800	Weak transcription	K562	blood
2	chr1:45758600-45763200	Weak transcription	Fetal Intestine Large	intestine
3	chr1:45759000-45763200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:45760400-45764400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:45761600-45763200	Enhancers	HepG2	liver
6	chr1:45761800-45764400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:45762600-45768400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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