Variant report

Variant	rs62279860
Chromosome Location	chr3:160960011-160960012
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160959557..160961368-chr3:160962963..160965074,2	MCF-7	breast:
2	chr3:160732451..160734009-chr3:160957436..160960399,2	MCF-7	breast:
3	chr3:160956099..160961317-chr3:160961958..160964988,5	K562	blood:
4	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs12488037	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12488318	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494261	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12494844	0.83[ASN][1000 genomes]
rs13318781	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13320863	0.82[ASN][1000 genomes]
rs1471440	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1478567	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs163138	0.81[ASN][1000 genomes]
rs1970834	0.82[ASN][1000 genomes]
rs336544	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs336545	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs336546	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs336564	0.81[ASN][1000 genomes]
rs336565	0.81[ASN][1000 genomes]
rs336566	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336573	0.80[ASN][1000 genomes]
rs336574	0.80[ASN][1000 genomes]
rs336576	0.80[ASN][1000 genomes]
rs336581	0.81[ASN][1000 genomes]
rs336584	0.81[ASN][1000 genomes]
rs336587	0.81[ASN][1000 genomes]
rs336588	0.81[ASN][1000 genomes]
rs336592	0.81[ASN][1000 genomes]
rs4270539	0.83[ASN][1000 genomes]
rs4429651	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4487256	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490410	0.83[ASN][1000 genomes]
rs57201455	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62278031	0.83[ASN][1000 genomes]
rs62278055	0.99[ASN][1000 genomes]
rs62279861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62279892	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73160351	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73160362	1.00[ASN][1000 genomes]
rs73162530	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9290072	0.91[ASN][1000 genomes]
rs9290075	0.92[ASN][1000 genomes]
rs978933	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9811833	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9812083	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9818516	0.85[ASN][1000 genomes]
rs9825118	0.83[ASN][1000 genomes]
rs9827833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9828189	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9828231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9831725	0.97[ASN][1000 genomes]
rs9836094	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839404	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9842281	0.83[ASN][1000 genomes]
rs9857946	0.91[ASN][1000 genomes]
rs9858399	0.83[ASN][1000 genomes]
rs9859045	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9876553	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9878365	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160940000-160971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160940200-160965400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:160941000-160969600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:160941000-160970200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:160941000-160974800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
9	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
10	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
11	chr3:160941200-160968600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:160941200-160969800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:160941200-160973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:160941400-160971800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:160941600-160969800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:160941600-160975400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:160941800-160975200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:160942000-160964000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:160942200-160973200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:160942400-160975200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:160942600-160965400	Weak transcription	Gastric	stomach
22	chr3:160942600-160971800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:160942600-160972600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:160942600-160973400	Strong transcription	Fetal Thymus	thymus
25	chr3:160942600-160975000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:160942600-160976600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:160942800-160971800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:160942800-160973800	Strong transcription	NH-A	brain
29	chr3:160942800-160978000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:160943000-160961600	Strong transcription	K562	blood
31	chr3:160943000-160965400	Weak transcription	Right Ventricle	heart
32	chr3:160943600-160963200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:160943600-160963200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:160943600-160977200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:160945000-160961400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:160945200-160964200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:160945600-160965200	Weak transcription	Fetal Intestine Small	intestine
38	chr3:160946400-160972800	Strong transcription	HSMM	muscle
39	chr3:160946600-160963400	Strong transcription	HepG2	liver
40	chr3:160947000-160961800	Weak transcription	Psoas Muscle	Psoas
41	chr3:160947000-160965800	Weak transcription	Brain Angular Gyrus	brain
42	chr3:160947200-160972600	Weak transcription	Stomach Mucosa	stomach
43	chr3:160947400-160967600	Weak transcription	Fetal Brain Male	brain
44	chr3:160947400-160973600	Strong transcription	HUVEC	blood vessel
45	chr3:160947600-160967000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:160948000-160965000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:160948600-160962000	Weak transcription	Brain Germinal Matrix	brain
48	chr3:160948800-160965400	Weak transcription	Thymus	Thymus
49	chr3:160948800-160971600	Weak transcription	Aorta	Aorta
50	chr3:160948800-160978000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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