Variant report

Variant	rs1979646
Chromosome Location	chr5:53213265-53213266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:53213246..53216350-chr5:53221900..53224479,3	K562	blood:
2	chr5:52778498..52779302-chr5:53212998..53213560,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134363	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1027210	0.83[AMR][1000 genomes]
rs175248	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979647	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1981842	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2035771	0.89[AMR][1000 genomes]
rs2042313	0.82[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs271207	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs271208	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs271243	1.00[EUR][1000 genomes]
rs271245	1.00[EUR][1000 genomes]
rs271250	1.00[EUR][1000 genomes]
rs271257	1.00[EUR][1000 genomes]
rs271261	1.00[EUR][1000 genomes]
rs37539	1.00[EUR][1000 genomes]
rs37540	1.00[EUR][1000 genomes]
rs3776740	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3797287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3797290	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs40211	1.00[EUR][1000 genomes]
rs40212	1.00[EUR][1000 genomes]
rs6450173	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs702616	0.82[AMR][1000 genomes]
rs7733347	0.83[AMR][1000 genomes];1.00[EUR][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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv533778	chr5:53092696-53284566	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53173800-53227800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:53187600-53232800	Weak transcription	Primary T cells from cord blood	blood
3	chr5:53189800-53216600	Weak transcription	Left Ventricle	heart
4	chr5:53200800-53251600	Weak transcription	Primary B cells from cord blood	blood
5	chr5:53206800-53236600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:53208200-53215000	Weak transcription	Fetal Brain Female	brain
7	chr5:53212400-53213600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:53212600-53213800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:53212600-53213800	Enhancers	NHDF-Ad	bronchial
10	chr5:53212800-53213400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:53212800-53213400	Enhancers	NHEK	skin
12	chr5:53212800-53213400	Enhancers	Osteobl	bone
13	chr5:53212800-53213600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:53212800-53213600	Enhancers	Fetal Heart	heart
15	chr5:53212800-53213600	Enhancers	HSMM	muscle
16	chr5:53212800-53213800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:53212800-53213800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:53212800-53213800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:53212800-53213800	Enhancers	Fetal Intestine Small	intestine
20	chr5:53212800-53213800	Enhancers	A549	lung
21	chr5:53212800-53213800	Enhancers	NH-A	brain
22	chr5:53212800-53214000	Enhancers	K562	blood
23	chr5:53213000-53213600	Enhancers	Rectal Smooth Muscle	rectum
24	chr5:53213000-53213800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:53213000-53213800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:53213000-53214000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:53213200-53213600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:53213200-53213600	Enhancers	NHLF	lung
29	chr5:53213200-53213800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:53213200-53213800	Enhancers	Fetal Stomach	stomach

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