Variant report

Variant	rs6550874
Chromosome Location	chr3:24528237-24528238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23957827..23959353-chr3:24527568..24529849,2	K562	blood:
2	chr3:24520353..24523433-chr3:24523948..24528616,5	MCF-7	breast:
3	chr3:24305072..24307020-chr3:24526305..24529102,2	K562	blood:
4	chr3:24518423..24520511-chr3:24527444..24530352,2	K562	blood:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs58016799	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6550875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73152104	0.90[AFR][1000 genomes]
rs73152107	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24509600-24531000	Weak transcription	Fetal Lung	lung
2	chr3:24515600-24533200	Weak transcription	Stomach Mucosa	stomach
3	chr3:24517800-24528600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:24517800-24529000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:24519400-24532800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:24520400-24529800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:24522600-24528600	Weak transcription	Adipose Nuclei	Adipose
8	chr3:24523000-24534000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:24524000-24529000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:24524000-24529400	Weak transcription	Ovary	ovary
11	chr3:24525200-24531800	Enhancers	Liver	Liver
12	chr3:24525600-24530800	Weak transcription	Spleen	Spleen
13	chr3:24525600-24531200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:24525600-24531800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:24525600-24533800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:24525800-24531000	Weak transcription	K562	blood
17	chr3:24526600-24529600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:24526600-24530200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr3:24526800-24534000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:24527000-24530200	Enhancers	HMEC	breast
21	chr3:24527200-24529800	Enhancers	Colon Smooth Muscle	Colon
22	chr3:24527200-24531200	Weak transcription	Hela-S3	cervix
23	chr3:24527400-24528800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:24527400-24529400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr3:24527600-24528800	Weak transcription	Fetal Intestine Small	intestine
26	chr3:24527600-24528800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:24527600-24528800	Weak transcription	HepG2	liver
28	chr3:24527600-24529600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:24527600-24531000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:24527600-24535400	Weak transcription	Lung	lung
31	chr3:24527800-24528400	Enhancers	NHDF-Ad	bronchial
32	chr3:24527800-24528600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:24527800-24528800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:24527800-24529000	Weak transcription	Psoas Muscle	Psoas
35	chr3:24527800-24529800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr3:24527800-24531600	Weak transcription	Brain Germinal Matrix	brain
37	chr3:24527800-24531600	Weak transcription	Right Atrium	heart
38	chr3:24527800-24531800	Weak transcription	Pancreas	Pancrea
39	chr3:24527800-24533600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:24528000-24528800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:24528000-24528800	Enhancers	Stomach Smooth Muscle	stomach
42	chr3:24528000-24529200	Weak transcription	Aorta	Aorta
43	chr3:24528000-24529400	Enhancers	Fetal Intestine Large	intestine
44	chr3:24528000-24531800	Weak transcription	Gastric	stomach
45	chr3:24528000-24532000	Weak transcription	Left Ventricle	heart
46	chr3:24528200-24530800	Weak transcription	Right Ventricle	heart

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