Variant report

Variant	rs12664535
Chromosome Location	chr6:57177666-57177667
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:57177321-57177671	IMR90	lung:	n/a	chr6:57177489-57177500
2	GATA3	chr6:57177650-57179171	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:57036717..57038735-chr6:57176806..57179766,2	K562	blood:
2	chr6:57177396..57179187-chr6:57179972..57181489,2	K562	blood:
3	chr6:56818167..56820292-chr6:57177596..57182762,4	MCF-7	breast:
4	chr6:57037957..57039628-chr6:57176354..57177855,2	MCF-7	breast:
5	chr6:57090172..57091708-chr6:57176939..57178620,2	K562	blood:

Variant related genes	Relation type
PRIM2	TF binding region
ENSG00000151914	Chromatin interaction
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000151917	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1013893	0.96[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs1013894	0.83[ASN][1000 genomes]
rs1019210	0.82[CHB][hapmap]
rs10733187	0.83[CHB][hapmap]
rs1119375	0.91[CHB][hapmap]
rs12176102	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1618210	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs1741916	0.82[CHB][hapmap]
rs1755833	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2013464	0.82[CHB][hapmap]
rs2098172	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2191651	0.91[CHB][hapmap]
rs3800015	0.89[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4712144	0.82[CHB][hapmap]
rs4712154	0.91[CHB][hapmap]
rs4715653	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715654	0.82[CHB][hapmap]
rs4715655	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs4715656	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715657	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs4715668	0.90[YRI][hapmap]
rs6459193	0.91[CHB][hapmap]
rs7754116	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7756422	0.87[CHB][hapmap]
rs7771738	0.80[CHB][hapmap]
rs887544	0.89[YRI][hapmap]
rs9357943	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs9357944	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357946	0.89[YRI][hapmap]
rs9382701	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9382736	0.90[CHB][hapmap]
rs9396278	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs980327	0.85[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57170400-57178200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:57171200-57178000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:57171400-57178000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:57171600-57178200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:57175800-57178000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:57176800-57181200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:57177000-57178200	Enhancers	HSMM	muscle
8	chr6:57177000-57178200	Enhancers	HSMMtube	muscle
9	chr6:57177000-57178600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr6:57177000-57181200	Enhancers	NHDF-Ad	bronchial
11	chr6:57177200-57177800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:57177200-57177800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:57177200-57178200	Enhancers	NH-A	brain
14	chr6:57177200-57179800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:57177400-57178200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:57177400-57178200	Enhancers	NHLF	lung
17	chr6:57177400-57178200	Enhancers	Osteobl	bone
18	chr6:57177400-57178400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:57177600-57177800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr6:57177600-57178000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:57177600-57178000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:57177600-57178200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:57177600-57178200	Enhancers	Fetal Kidney	kidney
24	chr6:57177600-57178800	Enhancers	Colon Smooth Muscle	Colon
25	chr6:57177600-57180000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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