Variant report

Variant	rs9860235
Chromosome Location	chr3:69245949-69245950
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69243953..69247149-chr3:69247614..69251113,3	MCF-7	breast:
2	chr3:69242995..69248050-chr3:69248288..69251594,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114541	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11128118	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11712024	0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12172924	0.98[ASN][1000 genomes]
rs12637416	0.90[JPT][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs13059488	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059687	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082480	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28529735	0.84[ASN][1000 genomes]
rs4282065	0.80[ASN][1000 genomes]
rs4358306	0.91[ASN][1000 genomes]
rs4464459	0.82[ASN][1000 genomes]
rs4473559	0.83[ASN][1000 genomes]
rs4493438	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4508787	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4541413	0.90[JPT][hapmap];0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4624565	1.00[CEU][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67268350	0.90[ASN][1000 genomes]
rs6763046	0.86[ASN][1000 genomes]
rs6765197	0.87[ASN][1000 genomes]
rs6765309	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6777671	0.87[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs6804718	0.88[ASN][1000 genomes]
rs7609655	0.80[ASN][1000 genomes]
rs7647940	0.87[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs9310139	0.80[ASN][1000 genomes]
rs9310140	0.82[ASN][1000 genomes]
rs9833167	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838728	0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9847983	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853318	0.89[ASN][1000 genomes]
rs9853587	0.90[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9853744	0.88[ASN][1000 genomes]
rs9872489	0.82[ASN][1000 genomes]
rs9875511	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	esv3398378	chr3:69240573-69271936	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69218400-69247400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:69218400-69247800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:69226800-69246800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:69228400-69246800	Weak transcription	Primary T cells from cord blood	blood
5	chr3:69228600-69248600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:69228800-69246000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:69229000-69248400	Weak transcription	Primary B cells from cord blood	blood
8	chr3:69229200-69246000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:69229600-69248200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:69230600-69248600	Weak transcription	Aorta	Aorta
11	chr3:69230600-69248600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:69230800-69248600	Weak transcription	Ovary	ovary
13	chr3:69231200-69246800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:69231200-69248600	Weak transcription	Left Ventricle	heart
15	chr3:69231200-69248600	Weak transcription	Small Intestine	intestine
16	chr3:69231400-69246400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:69231400-69246600	Weak transcription	Fetal Brain Male	brain
18	chr3:69231400-69248400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:69231400-69249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:69231600-69248600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:69231800-69249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:69232000-69247400	Weak transcription	Hela-S3	cervix
23	chr3:69232000-69248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:69232000-69249400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:69232000-69275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:69232200-69248600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:69232400-69246600	Strong transcription	Placenta	Placenta
28	chr3:69232400-69247400	Weak transcription	Stomach Mucosa	stomach
29	chr3:69232400-69248400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:69232400-69248400	Weak transcription	Brain Angular Gyrus	brain
31	chr3:69232600-69246000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:69232800-69249200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:69233200-69247200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:69233200-69247800	Strong transcription	Fetal Intestine Large	intestine
35	chr3:69233400-69246600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:69233600-69247400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr3:69233600-69247800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:69234000-69246600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:69234000-69248200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:69235800-69246600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr3:69236400-69248400	Weak transcription	HepG2	liver
42	chr3:69237000-69246800	Strong transcription	Liver	Liver
43	chr3:69238000-69246400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:69238200-69247000	Strong transcription	Dnd41	blood
45	chr3:69238200-69248400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:69239200-69246000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:69239200-69246400	Strong transcription	Fetal Thymus	thymus
48	chr3:69239600-69246600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:69239600-69247400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:69239600-69248000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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