Variant report

Variant	rs62285478
Chromosome Location	chr3:99822135-99822136
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	chr3:99781468..99783579-chr3:99820252..99822252,2	MCF-7	breast:
2	chr3:99820099..99823148-chr3:99826094..99828977,3	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10049383	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1017968	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212525	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1021341	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511177	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11537816	0.82[AMR][1000 genomes]
rs13064704	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069311	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093776	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13093838	0.81[AMR][1000 genomes]
rs13323143	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1489816	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17379739	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17392948	0.81[AMR][1000 genomes]
rs17393059	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291494	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291495	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28503408	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28714363	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28870092	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34922392	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996634	0.81[AMR][1000 genomes]
rs35154249	0.81[AMR][1000 genomes]
rs35521705	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35669453	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35844878	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35885423	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4279135	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4571265	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4928234	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62285461	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285462	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285471	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285473	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790535	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790877	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799379	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802422	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806178	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807176	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71313585	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610486	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620228	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627991	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923470	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs923471	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289985	0.82[AMR][1000 genomes]
rs9810235	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814359	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815439	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823908	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828079	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832186	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9833888	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9833980	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9834484	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9837602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9841186	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851645	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9852435	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9853823	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9854260	0.82[AMR][1000 genomes]
rs9860290	0.87[AMR][1000 genomes]
rs9864437	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873709	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9873878	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9875640	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9875664	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9875878	0.82[AMR][1000 genomes]
rs9878931	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99809200-99823000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:99809200-99824400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:99809800-99822400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:99809800-99824400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:99813000-99823000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:99813000-99823600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:99815200-99823000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:99816000-99822800	Weak transcription	Right Atrium	heart
10	chr3:99816000-99823000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:99817000-99822800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:99817000-99822800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:99817200-99823000	Weak transcription	Brain Substantia Nigra	brain
14	chr3:99817200-99824000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:99817400-99822800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:99817400-99822800	Weak transcription	Brain Anterior Caudate	brain
17	chr3:99817400-99822800	Weak transcription	Small Intestine	intestine
18	chr3:99817600-99822800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:99817600-99823400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:99817600-99825000	Weak transcription	Placenta	Placenta
21	chr3:99817800-99823400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:99818000-99823000	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:99818000-99824200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:99818000-99836600	Weak transcription	Primary B cells from cord blood	blood
25	chr3:99818200-99822600	Weak transcription	Stomach Mucosa	stomach
26	chr3:99818800-99822800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:99818800-99822800	Weak transcription	Fetal Intestine Large	intestine
28	chr3:99819400-99822800	Weak transcription	Esophagus	oesophagus
29	chr3:99819400-99822800	Weak transcription	HSMM	muscle
30	chr3:99819800-99822200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:99819800-99822800	Weak transcription	NHDF-Ad	bronchial
32	chr3:99820000-99822600	Weak transcription	NH-A	brain
33	chr3:99820200-99822400	Weak transcription	NHLF	lung
34	chr3:99820200-99822800	Weak transcription	Fetal Intestine Small	intestine
35	chr3:99820200-99823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:99820200-99825000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:99820400-99822400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:99821200-99823000	Enhancers	Aorta	Aorta
39	chr3:99821400-99822200	Enhancers	Fetal Muscle Leg	muscle
40	chr3:99821400-99822600	Enhancers	Adipose Nuclei	Adipose
41	chr3:99821400-99823600	Enhancers	Psoas Muscle	Psoas
42	chr3:99821400-99823600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr3:99821400-99823800	Weak transcription	Hela-S3	cervix
44	chr3:99821400-99824400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:99821600-99825200	Enhancers	HSMMtube	muscle
46	chr3:99821600-99826200	Enhancers	HepG2	liver
47	chr3:99821800-99822200	Enhancers	Fetal Heart	heart
48	chr3:99821800-99822200	Enhancers	Right Ventricle	heart
49	chr3:99821800-99822400	Enhancers	GM12878-XiMat	blood
50	chr3:99821800-99823600	Enhancers	Pancreas	Pancrea

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