Variant report

Variant	rs1354600
Chromosome Location	chr3:24401390-24401391
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:24400847..24401899-chr3:24681498..24682394,3	MCF-7	breast:
2	chr3:24305879..24306714-chr3:24400956..24401773,2	MCF-7	breast:
3	chr3:24309007..24309812-chr3:24400838..24401771,2	MCF-7	breast:
4	chr3:24389645..24392065-chr3:24400848..24403324,2	MCF-7	breast:
5	chr3:24400923..24401537-chr3:24537754..24538628,3	MCF-7	breast:
6	chr3:24392934..24395515-chr3:24399959..24401647,2	K562	blood:
7	chr3:24400983..24403336-chr3:24403755..24406100,3	K562	blood:
8	chr3:24399026..24404145-chr3:24535255..24539197,6	MCF-7	breast:
9	chr3:24400228..24405741-chr3:24531182..24533191,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1354599	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1354601	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1394763	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs17014547	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs56140521	0.87[EUR][1000 genomes]
rs59263745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789655	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs73043725	0.98[AFR][1000 genomes]
rs73043736	1.00[AFR][1000 genomes]
rs73043737	1.00[AFR][1000 genomes]
rs73825626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	chr3:24393600-24403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:24394000-24403200	Weak transcription	NHDF-Ad	bronchial
4	chr3:24394000-24406600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:24394000-24406600	Weak transcription	Ovary	ovary
6	chr3:24394000-24406600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:24394000-24407800	Weak transcription	Pancreas	Pancrea
8	chr3:24394000-24407800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:24394000-24431400	Weak transcription	Gastric	stomach
10	chr3:24394200-24403800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:24394400-24403000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:24394800-24401600	Weak transcription	Brain Substantia Nigra	brain
13	chr3:24395000-24404400	Weak transcription	Fetal Intestine Large	intestine
14	chr3:24395200-24404400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:24396400-24401600	Weak transcription	HepG2	liver
16	chr3:24398000-24404600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:24398200-24403800	Weak transcription	Fetal Intestine Small	intestine
18	chr3:24398200-24411800	Weak transcription	Psoas Muscle	Psoas
19	chr3:24399000-24402000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:24399200-24401800	Enhancers	Fetal Lung	lung
21	chr3:24399400-24401400	Weak transcription	Fetal Kidney	kidney
22	chr3:24399600-24406600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:24400400-24402600	Enhancers	Liver	Liver
24	chr3:24400400-24403000	Enhancers	Aorta	Aorta
25	chr3:24400400-24404600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:24400600-24401400	Enhancers	Left Ventricle	heart
27	chr3:24400600-24401400	Enhancers	K562	blood
28	chr3:24400800-24404400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:24401000-24401800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:24401000-24402200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr3:24401000-24402200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:24401000-24402400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr3:24401200-24401600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:24401200-24401800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:24401200-24401800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:24401200-24401800	Enhancers	Colon Smooth Muscle	Colon
37	chr3:24401200-24402000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:24401200-24402000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr3:24401200-24402000	Enhancers	H9 Cell Line	embryonic stem cell
40	chr3:24401200-24402600	Enhancers	HUES64 Cell Line	embryonic stem cell

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