Variant report

Variant	rs12259524
Chromosome Location	chr10:99334942-99334943
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99204433..99207263-chr10:99333172..99335779,3	MCF-7	breast:
2	chr10:99275538..99279686-chr10:99333593..99336127,3	MCF-7	breast:
3	chr10:99329733..99337149-chr10:99338392..99346753,19	MCF-7	breast:
4	chr10:99256533..99260506-chr10:99329939..99335950,10	MCF-7	breast:
5	chr10:99333671..99336639-chr10:99408320..99410860,2	MCF-7	breast:
6	chr10:99328694..99331523-chr10:99333360..99336351,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155229	Chromatin interaction
ENSG00000241935	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000165886	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000249967	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10882958	0.88[ASN][1000 genomes]
rs11189254	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12245837	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12256733	1.00[TSI][hapmap]
rs12263319	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263477	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17107905	0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17108072	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17108087	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17108114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17112803	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1889545	0.82[JPT][hapmap]
rs2153545	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2275588	0.88[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs35311829	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3814552	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4418736	0.82[JPT][hapmap]
rs4919098	0.82[JPT][hapmap]
rs4919110	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs58336429	0.93[ASN][1000 genomes]
rs59951048	1.00[ASN][1000 genomes]
rs60730732	0.93[ASN][1000 genomes]
rs7077096	1.00[ASN][1000 genomes]
rs7897051	0.86[CHB][hapmap]
rs7897232	0.86[CHB][hapmap]
rs7912825	0.88[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7915140	1.00[TSI][hapmap]
rs7922873	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928604	0.82[JPT][hapmap]
rs964733	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1047359	chr10:99306501-99369013	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99329800-99336000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr10:99330000-99335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:99330800-99335000	Weak transcription	Ovary	ovary
4	chr10:99330800-99335400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr10:99330800-99336200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr10:99330800-99336200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:99330800-99336200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr10:99331000-99337200	Enhancers	Fetal Heart	heart
9	chr10:99331400-99336000	Enhancers	Fetal Muscle Leg	muscle
10	chr10:99331400-99336200	Enhancers	Hela-S3	cervix
11	chr10:99332000-99335400	Enhancers	HMEC	breast
12	chr10:99332000-99335600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr10:99332000-99335800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr10:99332200-99335000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:99332200-99336200	Enhancers	NHEK	skin
16	chr10:99332400-99335000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr10:99332600-99335200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:99332600-99335600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:99332600-99338200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:99332800-99336200	Enhancers	HSMM	muscle
21	chr10:99333000-99336000	Enhancers	Fetal Muscle Trunk	muscle
22	chr10:99333200-99335600	Enhancers	HSMMtube	muscle
23	chr10:99333400-99336200	Enhancers	Placenta	Placenta
24	chr10:99333600-99335400	Enhancers	HUVEC	blood vessel
25	chr10:99333800-99335200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr10:99333800-99335200	Enhancers	Osteobl	bone
27	chr10:99333800-99335400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr10:99333800-99336200	Enhancers	Psoas Muscle	Psoas
29	chr10:99334000-99335400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:99334000-99336200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr10:99334200-99335000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr10:99334200-99335000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr10:99334200-99335000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr10:99334200-99335000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:99334200-99335000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:99334200-99335000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr10:99334200-99335000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:99334200-99335000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr10:99334200-99335000	Enhancers	Aorta	Aorta
40	chr10:99334200-99335000	Flanking Active TSS	A549	lung
41	chr10:99334200-99335000	Enhancers	NH-A	brain
42	chr10:99334200-99335200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr10:99334200-99335200	Enhancers	Liver	Liver
44	chr10:99334200-99335200	Enhancers	Fetal Kidney	kidney
45	chr10:99334200-99335200	Enhancers	NHDF-Ad	bronchial
46	chr10:99334200-99335400	Enhancers	Pancreas	Pancrea
47	chr10:99334200-99336000	Enhancers	Right Ventricle	heart
48	chr10:99334200-99336400	Enhancers	Left Ventricle	heart
49	chr10:99334400-99335000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr10:99334400-99335000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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