Variant report

Variant	rs60049973
Chromosome Location	chr3:119723404-119723405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119721357..119723738-chr3:119814057..119815870,3	MCF-7	breast:
2	chr3:119709355..119712243-chr3:119721755..119723709,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1037974	1.00[ASN][1000 genomes]
rs13314836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322562	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17246730	1.00[ASN][1000 genomes]
rs17246737	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1903764	1.00[ASN][1000 genomes]
rs28821007	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34002644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4491944	1.00[ASN][1000 genomes]
rs57027844	1.00[ASN][1000 genomes]
rs57132942	1.00[ASN][1000 genomes]
rs58299321	1.00[ASN][1000 genomes]
rs58371446	1.00[ASN][1000 genomes]
rs58991487	1.00[ASN][1000 genomes]
rs59368677	1.00[ASN][1000 genomes]
rs59703574	0.86[ASN][1000 genomes]
rs60325644	1.00[ASN][1000 genomes]
rs60993278	1.00[ASN][1000 genomes]
rs61188334	1.00[ASN][1000 genomes]
rs61511292	1.00[ASN][1000 genomes]
rs61566983	1.00[ASN][1000 genomes]
rs6796550	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs922337	1.00[ASN][1000 genomes]
rs9812149	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9834346	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9843795	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9849889	0.93[AFR][1000 genomes]
rs9853463	0.93[AFR][1000 genomes]
rs9865193	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9867915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9872321	0.93[AFR][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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119693600-119732200	Weak transcription	A549	lung
2	chr3:119710200-119730800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:119711400-119729200	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:119712000-119732200	Weak transcription	HepG2	liver
5	chr3:119712200-119732400	Weak transcription	NHLF	lung
6	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
7	chr3:119712800-119732200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
9	chr3:119717400-119730200	Weak transcription	Brain Anterior Caudate	brain
10	chr3:119717600-119732200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:119718200-119736800	Weak transcription	Liver	Liver
12	chr3:119719000-119729800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:119719600-119730000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:119720200-119731800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:119720200-119736600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:119720200-119741000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:119720400-119729600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:119720400-119730400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:119720400-119737200	Weak transcription	NHDF-Ad	bronchial
20	chr3:119720800-119730200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:119720800-119738600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:119721000-119724200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:119721000-119724400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr3:119721000-119731200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:119721000-119731200	Weak transcription	Fetal Lung	lung
26	chr3:119721400-119733600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:119722600-119723600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:119722600-119723600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:119722600-119723600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr3:119722600-119723600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:119722600-119723600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr3:119722600-119723600	Enhancers	Gastric	stomach
33	chr3:119722600-119723600	Enhancers	Left Ventricle	heart
34	chr3:119722600-119723800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:119722600-119723800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:119722600-119723800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:119722600-119723800	Enhancers	Fetal Thymus	thymus
38	chr3:119722600-119724000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:119722600-119724000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:119722600-119724200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:119722600-119724200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:119722800-119723600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:119722800-119723600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:119722800-119723600	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr3:119722800-119723600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:119722800-119723600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:119722800-119723600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:119722800-119723600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:119722800-119723600	Enhancers	Lung	lung
50	chr3:119722800-119723600	Enhancers	Right Ventricle	heart

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