Variant report

Variant	rs2397176
Chromosome Location	chr6:54775481-54775482
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	chr6:54711197..54712939-chr6:54774381..54776518,2	MCF-7	breast:
2	chr6:54712764..54715534-chr6:54774311..54776470,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1028423	1.00[ASN][1000 genomes]
rs1056630	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13216252	0.83[AFR][1000 genomes]
rs1503150	0.92[ASN][1000 genomes]
rs171226	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1738459	0.92[ASN][1000 genomes]
rs183011	1.00[ASN][1000 genomes]
rs239780	1.00[ASN][1000 genomes]
rs239787	0.92[ASN][1000 genomes]
rs239788	0.92[ASN][1000 genomes]
rs239789	0.92[ASN][1000 genomes]
rs239791	0.92[ASN][1000 genomes]
rs239793	0.92[ASN][1000 genomes]
rs239797	0.92[ASN][1000 genomes]
rs239798	0.92[ASN][1000 genomes]
rs239799	0.92[ASN][1000 genomes]
rs239802	0.92[ASN][1000 genomes]
rs239805	0.85[ASN][1000 genomes]
rs239807	0.92[ASN][1000 genomes]
rs239808	0.92[ASN][1000 genomes]
rs239810	0.92[ASN][1000 genomes]
rs239823	1.00[ASN][1000 genomes]
rs239824	1.00[ASN][1000 genomes]
rs239827	0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs239828	0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs239829	0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs239830	0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs239831	0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs239832	1.00[ASN][1000 genomes]
rs239833	1.00[ASN][1000 genomes]
rs239834	0.84[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs239835	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs239836	0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs239838	1.00[ASN][1000 genomes]
rs239839	1.00[ASN][1000 genomes]
rs239840	1.00[ASN][1000 genomes]
rs239841	1.00[ASN][1000 genomes]
rs239842	1.00[ASN][1000 genomes]
rs239843	1.00[ASN][1000 genomes]
rs239844	1.00[ASN][1000 genomes]
rs239845	1.00[ASN][1000 genomes]
rs239846	1.00[ASN][1000 genomes]
rs239847	1.00[ASN][1000 genomes]
rs239848	0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs239849	1.00[ASN][1000 genomes]
rs239851	0.92[ASN][1000 genomes]
rs239852	0.92[ASN][1000 genomes]
rs239853	0.92[ASN][1000 genomes]
rs2746440	0.92[ASN][1000 genomes]
rs35620314	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs378853	0.92[ASN][1000 genomes]
rs398483	0.92[ASN][1000 genomes]
rs406149	1.00[ASN][1000 genomes]
rs57835829	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59689523	0.84[ASN][1000 genomes]
rs6917766	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73431470	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743188	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7749972	0.92[ASN][1000 genomes]
rs7774568	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9475077	0.92[ASN][1000 genomes]

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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54765800-54780800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:54769000-54780800	Weak transcription	NHEK	skin
3	chr6:54770000-54781200	Weak transcription	HMEC	breast
4	chr6:54774600-54776600	Enhancers	Fetal Lung	lung
5	chr6:54774800-54781200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:54775000-54775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:54775000-54775600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:54775000-54775600	Active TSS	Brain Cingulate Gyrus	brain
9	chr6:54775000-54775600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr6:54775000-54775800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:54775000-54775800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr6:54775000-54776000	Enhancers	Fetal Intestine Large	intestine
13	chr6:54775000-54776000	Enhancers	Fetal Intestine Small	intestine
14	chr6:54775200-54775600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:54775200-54775600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:54775200-54775600	Enhancers	Brain Anterior Caudate	brain
17	chr6:54775200-54775600	Enhancers	Brain Germinal Matrix	brain
18	chr6:54775200-54775600	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr6:54775200-54775600	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr6:54775200-54775600	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr6:54775200-54775600	Enhancers	Stomach Mucosa	stomach
22	chr6:54775200-54775800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:54775200-54776000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:54775200-54776000	Enhancers	Fetal Brain Male	brain
25	chr6:54775400-54775600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:54775400-54775600	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr6:54775400-54775600	Active TSS	Duodenum Mucosa	Duodenum

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