Variant report

Variant	rs6550858
Chromosome Location	chr3:24409215-24409216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24408638..24410180-chr3:24416324..24419253,2	K562	blood:
2	chr3:24405318..24406958-chr3:24407481..24409434,2	K562	blood:
3	chr3:24408664..24412376-chr3:24534339..24537876,4	MCF-7	breast:
4	chr3:24401832..24411849-chr3:24534272..24539083,15	MCF-7	breast:
5	chr3:24406717..24408619-chr3:24408734..24410987,2	K562	blood:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13072812	0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078863	1.00[ASN][1000 genomes]
rs13086718	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095286	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394770	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62255386	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6774046	1.00[ASN][1000 genomes]
rs67870193	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71328474	1.00[ASN][1000 genomes]
rs73043744	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642291	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834640	chr3:24339779-24493605	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24360400-24418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:24394000-24431400	Weak transcription	Gastric	stomach
3	chr3:24398200-24411800	Weak transcription	Psoas Muscle	Psoas
4	chr3:24401400-24411800	Weak transcription	Left Ventricle	heart
5	chr3:24403800-24410400	Enhancers	Fetal Intestine Small	intestine
6	chr3:24404400-24410400	Enhancers	Stomach Mucosa	stomach
7	chr3:24404400-24410800	Enhancers	Fetal Intestine Large	intestine
8	chr3:24404800-24410200	Enhancers	HepG2	liver
9	chr3:24404800-24410400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr3:24405400-24410200	Enhancers	Duodenum Mucosa	Duodenum
11	chr3:24406600-24409400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:24406800-24411800	Weak transcription	Right Atrium	heart
13	chr3:24407400-24418400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:24407800-24412000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:24407800-24414400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:24407800-24414600	Weak transcription	Fetal Kidney	kidney
17	chr3:24408000-24412000	Weak transcription	NHDF-Ad	bronchial
18	chr3:24408200-24410200	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr3:24408400-24409400	Enhancers	Small Intestine	intestine
20	chr3:24408400-24409400	Enhancers	K562	blood
21	chr3:24408400-24410000	Enhancers	Stomach Smooth Muscle	stomach
22	chr3:24408400-24410200	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr3:24408400-24411800	Weak transcription	Pancreas	Pancrea
24	chr3:24408600-24409400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:24408600-24409600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:24408600-24409600	Enhancers	Liver	Liver
27	chr3:24408600-24409800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr3:24408600-24410000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr3:24408600-24410200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr3:24408800-24409400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:24408800-24409400	Enhancers	Aorta	Aorta
32	chr3:24408800-24410000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:24408800-24412000	Enhancers	Rectal Smooth Muscle	rectum
34	chr3:24409000-24409400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:24409000-24409400	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr3:24409000-24409400	Enhancers	Fetal Lung	lung
37	chr3:24409000-24409400	Enhancers	NHEK	skin
38	chr3:24409200-24409400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:24409200-24409600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:24409200-24416400	Weak transcription	A549	lung

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