Variant report

Variant	rs57439200
Chromosome Location	chr6:56501329-56501330
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	chr6:56491750..56493624-chr6:56500247..56502327,2	MCF-7	breast:
2	chr6:56500150..56502266-chr6:56506486..56508241,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1323321	1.00[AMR][1000 genomes]
rs4413617	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4520018	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57183853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57936670	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58912662	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59493539	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59643604	0.91[AFR][1000 genomes]
rs59801210	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60143048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60172134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60304191	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60620079	1.00[AMR][1000 genomes]
rs61396940	1.00[AFR][1000 genomes]
rs7753074	0.91[AFR][1000 genomes];1.00[AMR][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
2	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
3	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
4	chr6:56451800-56514200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:56452200-56514600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:56453000-56502200	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr6:56453000-56506800	Strong transcription	HSMM	muscle
8	chr6:56459000-56502400	Strong transcription	Osteobl	bone
9	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
10	chr6:56460600-56513600	Weak transcription	Stomach Mucosa	stomach
11	chr6:56470600-56502200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:56470800-56502600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:56478000-56502600	Strong transcription	NHDF-Ad	bronchial
14	chr6:56478200-56501600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:56478400-56514600	Weak transcription	Lung	lung
16	chr6:56478600-56501800	Strong transcription	Adipose Nuclei	Adipose
17	chr6:56479400-56502600	Strong transcription	HMEC	breast
18	chr6:56480000-56501800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:56480600-56514600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:56480800-56536400	Weak transcription	Gastric	stomach
21	chr6:56481000-56501600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:56482000-56518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:56482200-56501600	Strong transcription	Brain Anterior Caudate	brain
24	chr6:56482200-56505000	Weak transcription	Esophagus	oesophagus
25	chr6:56483400-56512600	Weak transcription	Psoas Muscle	Psoas
26	chr6:56485000-56514400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:56485600-56507400	Weak transcription	Aorta	Aorta
28	chr6:56485800-56512400	Weak transcription	Fetal Stomach	stomach
29	chr6:56487200-56501800	Strong transcription	Fetal Lung	lung
30	chr6:56487200-56502000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:56487600-56501800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:56488200-56501800	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:56488800-56501600	Strong transcription	HSMMtube	muscle
34	chr6:56488800-56507200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:56489000-56501600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:56489200-56501800	Strong transcription	NHLF	lung
37	chr6:56490000-56501600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:56490000-56513600	Strong transcription	Fetal Intestine Large	intestine
39	chr6:56490400-56507400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:56490600-56502600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:56490800-56507400	Strong transcription	Liver	Liver
42	chr6:56491600-56501600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:56491600-56536600	Weak transcription	Fetal Brain Female	brain
44	chr6:56493000-56502600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:56494800-56501800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:56495000-56501800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:56495200-56501600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:56495200-56501600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr6:56495200-56501800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:56495200-56501800	Strong transcription	Placenta	Placenta

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