Variant report

Variant	rs60272712
Chromosome Location	chr3:119732508-119732509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119730742..119733006-chr3:119735849..119738068,2	MCF-7	breast:
2	chr3:119729710..119735147-chr3:119812192..119816098,5	MCF-7	breast:
3	chr3:119717638..119719374-chr3:119730328..119732914,2	MCF-7	breast:
4	chr3:119730961..119733403-chr3:119813140..119815565,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1154596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1154597	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11921053	1.00[ASN][1000 genomes]
rs13312998	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626696	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16830683	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719888	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719895	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1732165	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1732169	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs182839	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs184576	0.85[EUR][1000 genomes]
rs2461827	0.91[ASN][1000 genomes]
rs3108749	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334534	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334536	0.94[ASN][1000 genomes]
rs334551	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs334552	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334554	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334560	0.94[ASN][1000 genomes]
rs334561	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334566	0.94[ASN][1000 genomes]
rs3853592	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4438691	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4605584	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688043	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56126162	0.84[ASN][1000 genomes]
rs58043853	0.81[ASN][1000 genomes]
rs6438554	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438555	0.94[ASN][1000 genomes]
rs66650215	0.97[ASN][1000 genomes]
rs6762640	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769435	0.84[ASN][1000 genomes]
rs6770314	0.84[ASN][1000 genomes]
rs6771023	1.00[ASN][1000 genomes]
rs6774693	1.00[ASN][1000 genomes]
rs6784239	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785050	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795874	0.84[ASN][1000 genomes]
rs6797689	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6805931	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6807868	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613197	0.84[ASN][1000 genomes]
rs7624540	0.91[ASN][1000 genomes]
rs7628426	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7635604	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636600	1.00[ASN][1000 genomes]
rs7650554	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289138	0.84[ASN][1000 genomes]
rs968824	0.94[ASN][1000 genomes]
rs9784393	0.85[EUR][1000 genomes]
rs9879992	0.84[ASN][1000 genomes]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
2	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
3	chr3:119718200-119736800	Weak transcription	Liver	Liver
4	chr3:119720200-119736600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:119720200-119741000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:119720400-119737200	Weak transcription	NHDF-Ad	bronchial
7	chr3:119720800-119738600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:119721400-119733600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:119723200-119734800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:119723200-119736200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:119723600-119740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:119724000-119736800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:119724000-119738200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:119724000-119741400	Weak transcription	Thymus	Thymus
15	chr3:119724200-119734600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:119729200-119732600	Enhancers	Colon Smooth Muscle	Colon
17	chr3:119729800-119733000	Enhancers	Brain Cingulate Gyrus	brain
18	chr3:119729800-119734000	Enhancers	Brain Substantia Nigra	brain
19	chr3:119730000-119743000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:119730000-119743000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:119730400-119732600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:119730600-119733800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:119730600-119736200	Weak transcription	Stomach Mucosa	stomach
24	chr3:119730600-119736400	Weak transcription	Small Intestine	intestine
25	chr3:119730600-119739200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:119730600-119740800	Weak transcription	Left Ventricle	heart
27	chr3:119730600-119741600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:119730800-119732600	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:119730800-119736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:119731000-119741400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:119731200-119732600	Enhancers	Fetal Heart	heart
32	chr3:119731200-119732800	Enhancers	Fetal Lung	lung
33	chr3:119731200-119736800	Weak transcription	Adipose Nuclei	Adipose
34	chr3:119731400-119752400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:119731600-119732600	Enhancers	Brain Angular Gyrus	brain
36	chr3:119731600-119737200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:119731800-119732600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:119731800-119732600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:119731800-119732600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:119731800-119732600	Enhancers	HSMMtube	muscle
41	chr3:119731800-119733400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:119731800-119733800	Enhancers	Brain Hippocampus Middle	brain
43	chr3:119731800-119737000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:119731800-119739800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:119732000-119732600	Enhancers	Brain Anterior Caudate	brain
46	chr3:119732000-119732600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr3:119732000-119732600	Enhancers	HSMM	muscle
48	chr3:119732000-119732800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:119732000-119733000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:119732000-119734000	Enhancers	Primary T helper cells fromperipheralblood	blood

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