Variant report

Variant	rs12853894
Chromosome Location	chr13:30279662-30279663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30163838..30166172-chr13:30279497..30282436,2	K562	blood:
2	chr13:30164682..30166932-chr13:30278422..30280468,2	MCF-7	breast:
3	chr13:30167909..30169969-chr13:30279599..30282032,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10220050	1.00[ASN][1000 genomes]
rs10220112	1.00[ASN][1000 genomes]
rs10492457	1.00[ASN][1000 genomes]
rs12854608	0.87[EUR][1000 genomes]
rs12864282	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12865724	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12866411	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12868072	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12872620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12872872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12873674	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12877965	1.00[CEU][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]
rs13378487	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13378570	1.00[ASN][1000 genomes]
rs17587218	1.00[ASN][1000 genomes]
rs2036973	1.00[ASN][1000 genomes]
rs2669038	1.00[ASN][1000 genomes]
rs3011607	1.00[ASN][1000 genomes]
rs34117941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34148142	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34220342	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34492142	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34879256	0.85[AFR][1000 genomes]
rs34967062	1.00[ASN][1000 genomes]
rs34973257	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34978805	1.00[ASN][1000 genomes]
rs35033033	1.00[ASN][1000 genomes]
rs35227498	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35566813	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35569918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35587642	0.92[AFR][1000 genomes]
rs35809262	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35820783	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901321	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs478085	1.00[ASN][1000 genomes]
rs555913	1.00[ASN][1000 genomes]
rs71427274	1.00[ASN][1000 genomes]
rs71427278	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71427279	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71427280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71434735	1.00[ASN][1000 genomes]
rs71434744	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71434746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71434747	1.00[AFR][1000 genomes]
rs7320198	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73448295	1.00[ASN][1000 genomes]
rs73454227	1.00[ASN][1000 genomes]
rs74042848	1.00[ASN][1000 genomes]
rs7986326	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991247	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7991463	1.00[ASN][1000 genomes]
rs7992028	1.00[ASN][1000 genomes]
rs7992839	1.00[ASN][1000 genomes]
rs7998704	1.00[ASN][1000 genomes]
rs9314960	1.00[ASN][1000 genomes]
rs9314961	1.00[ASN][1000 genomes]
rs9314962	1.00[ASN][1000 genomes]
rs9314964	1.00[ASN][1000 genomes]
rs9314968	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578108	1.00[ASN][1000 genomes]
rs9578110	1.00[ASN][1000 genomes]
rs9578112	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9578114	1.00[YRI][hapmap]
rs9578118	1.00[ASN][1000 genomes]
rs9578121	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578122	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578123	1.00[ASN][1000 genomes]
rs9578125	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578127	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578128	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578130	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578131	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578133	1.00[CEU][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]
rs9578134	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579405	1.00[ASN][1000 genomes]
rs9579406	1.00[ASN][1000 genomes]
rs9579407	1.00[ASN][1000 genomes]
rs9579408	1.00[ASN][1000 genomes]
rs9579410	1.00[ASN][1000 genomes]
rs9579411	1.00[ASN][1000 genomes]
rs9579413	1.00[ASN][1000 genomes]
rs9579414	1.00[ASN][1000 genomes]
rs9579417	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9579418	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9579419	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9579424	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9579425	1.00[ASN][1000 genomes]
rs9579428	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9579439	1.00[ASN][1000 genomes]
rs9579440	0.80[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9579442	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579445	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579446	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579447	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579449	0.85[AFR][1000 genomes]
rs9579451	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579454	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579455	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579457	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579459	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579462	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579463	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579464	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579465	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579468	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579469	0.87[EUR][1000 genomes]
rs9579470	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579472	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30277400-30280600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:30277600-30280200	Enhancers	NHDF-Ad	bronchial
3	chr13:30277800-30280200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:30278200-30280000	Weak transcription	Esophagus	oesophagus
5	chr13:30278600-30279800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:30278600-30279800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr13:30278800-30281600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:30278800-30283400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:30279000-30281200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr13:30279000-30281800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr13:30279200-30281200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr13:30279200-30281600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:30279600-30280200	Weak transcription	Spleen	Spleen
14	chr13:30279600-30281600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:30279600-30281800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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