Variant report

Variant	rs9816509
Chromosome Location	chr3:24431566-24431567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24431310..24433728-chr3:24534958..24537057,2	MCF-7	breast:
2	chr3:24339862..24342490-chr3:24429222..24432079,2	K562	blood:
3	chr3:24429881..24432866-chr3:24437467..24439284,2	MCF-7	breast:
4	chr3:24428751..24431920-chr3:24433157..24435631,4	K562	blood:

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11129150	0.91[EUR][1000 genomes]
rs11129152	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918018	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12495379	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13065876	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13086388	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1505286	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1505287	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1505289	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs17014597	0.85[ASN][1000 genomes]
rs17014605	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135147	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2217883	0.96[CEU][hapmap]
rs28380451	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35340172	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4276128	0.91[EUR][1000 genomes]
rs4300958	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4309672	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4423711	0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs4491844	0.87[ASN][1000 genomes]
rs4541352	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4602332	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4630886	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4858608	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858610	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4858613	0.96[CEU][hapmap]
rs6550865	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6769978	0.99[ASN][1000 genomes]
rs6771995	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6786474	0.93[ASN][1000 genomes]
rs7611219	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs7630858	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648757	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9310739	0.90[EUR][1000 genomes]
rs9310740	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9826887	0.89[EUR][1000 genomes]
rs9839986	0.96[CEU][hapmap]
rs9851523	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs9852824	0.84[CEU][hapmap];0.91[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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24420200-24441600	Weak transcription	Liver	Liver
2	chr3:24427000-24432400	Weak transcription	Lung	lung
3	chr3:24427000-24433000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:24427800-24432000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:24428000-24431600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:24428000-24432200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:24428000-24432200	Enhancers	HMEC	breast
8	chr3:24428200-24431800	Enhancers	NHEK	skin
9	chr3:24428600-24431600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:24428600-24431800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr3:24428600-24432000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:24428600-24432800	Enhancers	Colon Smooth Muscle	Colon
13	chr3:24428800-24432400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:24428800-24432800	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:24429000-24431800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:24429000-24432600	Enhancers	HSMMtube	muscle
17	chr3:24429000-24432800	Enhancers	Adipose Nuclei	Adipose
18	chr3:24429000-24432800	Enhancers	Pancreas	Pancrea
19	chr3:24429200-24432600	Enhancers	Stomach Smooth Muscle	stomach
20	chr3:24429200-24432800	Enhancers	Fetal Intestine Large	intestine
21	chr3:24429200-24432800	Enhancers	Left Ventricle	heart
22	chr3:24429600-24432600	Enhancers	Ovary	ovary
23	chr3:24429600-24433400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr3:24429800-24432200	Enhancers	HSMM	muscle
25	chr3:24429800-24432400	Enhancers	Fetal Intestine Small	intestine
26	chr3:24429800-24432800	Enhancers	Fetal Lung	lung
27	chr3:24429800-24432800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:24430000-24432800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr3:24430200-24431600	Enhancers	Esophagus	oesophagus
30	chr3:24430400-24431600	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr3:24430400-24432000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:24430400-24437200	Weak transcription	K562	blood
33	chr3:24430600-24431600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:24430600-24431600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:24430600-24431600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr3:24430600-24431800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr3:24430600-24431800	Enhancers	H9 Cell Line	embryonic stem cell
38	chr3:24430600-24431800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:24430600-24431800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:24430600-24432200	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr3:24430600-24432200	Enhancers	Stomach Mucosa	stomach
42	chr3:24430600-24432600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:24430600-24432600	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:24430600-24432600	Enhancers	Fetal Stomach	stomach
45	chr3:24430600-24443600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:24430800-24432000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr3:24430800-24432200	Enhancers	Fetal Kidney	kidney
48	chr3:24430800-24432600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr3:24430800-24434800	Weak transcription	Psoas Muscle	Psoas
50	chr3:24431000-24431800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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