Variant report

Variant	rs6457144
Chromosome Location	chr6:30063368-30063369
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30058600..30061539-chr6:30062741..30064895,3	MCF-7	breast:
2	chr6:30058142..30060356-chr6:30062997..30064640,2	MCF-7	breast:
3	chr6:30040732..30043488-chr6:30062276..30064354,2	K562	blood:
4	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
5	chr6:30036068..30037732-chr6:30063349..30066200,2	MCF-7	breast:
6	chr6:30033726..30035867-chr6:30063166..30065210,2	MCF-7	breast:
7	chr6:30041901..30046365-chr6:30059553..30065121,9	MCF-7	breast:
8	chr6:30039555..30048654-chr6:30056865..30065735,15	MCF-7	breast:
9	chr6:30039304..30041261-chr6:30060958..30063803,2	MCF-7	breast:
10	chr6:30053423..30056076-chr6:30062128..30065252,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204618	Chromatin interaction
ENSG00000204619	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1111180	0.82[AMR][1000 genomes]
rs2057728	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2394736	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132682	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6904455	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6909253	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6909437	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7382061	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9261394	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261395	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv884052	chr6:30059592-30067681	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv884053	chr6:30059592-30070538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
6	nsv884054	chr6:30061361-30069525	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6457144	KIT	trans	multi-tissue	Pritchard
rs6457144	BTN2A1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30060000-30064800	Weak transcription	Gastric	stomach
2	chr6:30060200-30065600	Weak transcription	Spleen	Spleen
3	chr6:30060400-30065200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:30061000-30066800	Enhancers	Stomach Mucosa	stomach
5	chr6:30062000-30063800	Enhancers	Duodenum Mucosa	Duodenum
6	chr6:30062000-30067000	Enhancers	Fetal Intestine Small	intestine
7	chr6:30062200-30067800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:30062600-30064800	Enhancers	Fetal Intestine Large	intestine
9	chr6:30062800-30064000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:30063000-30063400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:30063000-30063400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:30063000-30063600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:30063000-30063600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:30063000-30063600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:30063000-30063600	Bivalent Enhancer	HUVEC	blood vessel
16	chr6:30063000-30063800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:30063000-30063800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:30063000-30063800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:30063000-30063800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:30063000-30063800	Bivalent Enhancer	Brain Hippocampus Middle	brain
21	chr6:30063000-30063800	Enhancers	Placenta	Placenta
22	chr6:30063000-30063800	Bivalent Enhancer	Small Intestine	intestine
23	chr6:30063000-30063800	Enhancers	Hela-S3	cervix
24	chr6:30063000-30063800	Bivalent Enhancer	NHDF-Ad	bronchial
25	chr6:30063000-30063800	Enhancers	NHEK	skin
26	chr6:30063000-30063800	Enhancers	Osteobl	bone
27	chr6:30063000-30064000	Flanking Active TSS	HepG2	liver
28	chr6:30063200-30063600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:30063200-30063600	Bivalent Enhancer	Brain Substantia Nigra	brain
30	chr6:30063200-30063600	Enhancers	HMEC	breast
31	chr6:30063200-30063600	Enhancers	HSMMtube	muscle
32	chr6:30063200-30063800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:30063200-30063800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:30063200-30063800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
35	chr6:30063200-30063800	Flanking Active TSS	A549	lung

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