Variant report

Variant	rs4296611
Chromosome Location	chr3:160936458-160936459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160929000..160932392-chr3:160935549..160937889,3	K562	blood:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
4	chr3:160919833..160921562-chr3:160936344..160938437,2	K562	blood:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1017799	0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12486069	0.90[ASN][1000 genomes]
rs12489004	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12489125	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12490149	0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12494725	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12496235	0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13315320	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13319558	0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13319771	0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16831799	0.85[AMR][1000 genomes]
rs16831850	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16831864	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16831882	0.90[ASN][1000 genomes]
rs16831942	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2306209	0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28451189	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28704960	0.90[ASN][1000 genomes]
rs28713364	0.97[AMR][1000 genomes]
rs3925722	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4352387	0.88[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4468992	0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4580574	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4635725	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57903480	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59567999	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59593286	0.83[AMR][1000 genomes]
rs59757775	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59776766	0.90[ASN][1000 genomes]
rs59867530	0.82[AMR][1000 genomes]
rs60121330	0.90[ASN][1000 genomes]
rs6441350	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6441363	0.89[JPT][hapmap];0.94[AMR][1000 genomes]
rs6441365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441372	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6441375	0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6762064	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6771581	0.83[AMR][1000 genomes]
rs6774919	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6775446	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6775931	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6778186	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6782415	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6782518	0.88[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6785714	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6787447	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6788738	0.97[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6790805	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6796168	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6801664	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6805976	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73017340	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026933	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026967	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026968	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026983	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026987	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026989	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73878309	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7615833	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7615868	1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7624791	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7626773	0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7634299	0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7651924	0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7652624	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9290070	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9290071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9682249	0.85[AMR][1000 genomes]
rs9810351	0.90[ASN][1000 genomes]
rs9812574	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9818470	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9818835	0.90[ASN][1000 genomes]
rs9818992	0.85[ASN][1000 genomes]
rs9819793	0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9822705	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9822916	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9823424	0.90[ASN][1000 genomes]
rs9824535	0.90[ASN][1000 genomes]
rs9824805	0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9826857	0.90[ASN][1000 genomes]
rs9830183	0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9833270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9834806	0.94[AMR][1000 genomes]
rs9835530	0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9838945	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9841871	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9842290	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9847842	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9851699	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9855112	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9855572	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9856742	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9858907	0.90[ASN][1000 genomes]
rs9859641	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9860980	0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9862867	0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9871753	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9876077	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9877309	0.84[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9880536	0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9884100	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9985364	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160926000-160938400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:160931000-160938600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:160931800-160937200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:160931800-160938400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:160933200-160939000	Weak transcription	Gastric	stomach
6	chr3:160933400-160938600	Weak transcription	Stomach Mucosa	stomach
7	chr3:160933600-160938400	Weak transcription	Fetal Intestine Large	intestine
8	chr3:160935200-160937000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:160935600-160938000	Weak transcription	Hela-S3	cervix
10	chr3:160935600-160938400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:160935800-160938200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:160935800-160938200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:160935800-160938200	Weak transcription	HepG2	liver
14	chr3:160935800-160938200	Weak transcription	NHDF-Ad	bronchial
15	chr3:160935800-160938400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:160935800-160938600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:160936000-160938200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:160936000-160938200	Weak transcription	Osteobl	bone
19	chr3:160936000-160938400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:160936000-160938600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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