Variant report

Variant	rs9868889
Chromosome Location	chr3:50673010-50673011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50658918..50663131-chr3:50672291..50676051,5	K562	blood:
2	chr3:50658169..50660186-chr3:50671108..50673991,2	MCF-7	breast:
3	chr3:50653782..50659891-chr3:50667242..50673193,6	K562	blood:
4	chr3:50653782..50658590-chr3:50669577..50673193,4	K562	blood:
5	chr3:50671203..50673745-chr3:50674987..50677707,3	K562	blood:
6	chr3:50665770..50667653-chr3:50672418..50674764,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1013233	0.83[AFR][1000 genomes]
rs1077215	0.93[ASN][1000 genomes]
rs12486143	0.86[AMR][1000 genomes]
rs12486717	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12487817	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12489607	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12491440	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12491812	0.89[AMR][1000 genomes]
rs12492093	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12492540	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12492982	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12494094	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12494326	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12495399	0.83[ASN][1000 genomes]
rs1385025	0.81[AFR][1000 genomes]
rs17050991	0.89[AMR][1000 genomes]
rs17050995	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17051000	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17051043	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17051045	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17051403	0.88[ASN][1000 genomes]
rs1872184	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1894459	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1971976	0.81[AFR][1000 genomes]
rs201193	0.84[AFR][1000 genomes]
rs2035484	0.88[ASN][1000 genomes]
rs2076927	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2170840	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2227292	0.90[ASN][1000 genomes]
rs2227293	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2239750	0.90[ASN][1000 genomes]
rs2239751	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2239752	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2239753	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2269505	0.80[AFR][1000 genomes]
rs2285090	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34848480	0.82[AFR][1000 genomes]
rs3749265	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3752449	0.90[ASN][1000 genomes]
rs375544	0.87[AFR][1000 genomes]
rs3792323	0.95[ASN][1000 genomes]
rs3792325	0.85[AFR][1000 genomes]
rs3792328	0.87[AFR][1000 genomes]
rs3804632	0.88[AFR][1000 genomes]
rs3943212	0.81[AFR][1000 genomes]
rs396302	0.88[AFR][1000 genomes]
rs443436	0.85[AFR][1000 genomes]
rs4476497	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448028	0.88[AFR][1000 genomes]
rs453570	0.83[AFR][1000 genomes]
rs4640555	0.82[ASN][1000 genomes]
rs4688705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4688707	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4688709	0.90[ASN][1000 genomes]
rs4688710	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4688713	0.86[AMR][1000 genomes]
rs56170012	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56856095	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs57910827	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58427389	0.98[ASN][1000 genomes]
rs58529408	0.88[ASN][1000 genomes]
rs59036236	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60552073	0.81[AMR][1000 genomes]
rs60877431	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61193866	0.89[AMR][1000 genomes]
rs61316441	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61574029	0.90[AMR][1000 genomes]
rs61613532	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs616589	0.87[AFR][1000 genomes]
rs616689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6446208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6446212	0.81[AFR][1000 genomes]
rs650655	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6766638	0.87[AMR][1000 genomes]
rs6771348	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6783922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6794155	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs728901	0.83[AFR][1000 genomes]
rs728902	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72938758	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72942785	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72942794	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72944726	0.88[ASN][1000 genomes]
rs72944730	0.88[ASN][1000 genomes]
rs73835531	0.86[AMR][1000 genomes]
rs743753	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs745356	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs751851	0.82[AFR][1000 genomes]
rs762889	0.90[ASN][1000 genomes]
rs7646236	0.81[AFR][1000 genomes]
rs808148	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs808149	0.83[AFR][1000 genomes]
rs813243	0.85[AFR][1000 genomes]
rs876103	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs876104	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs876105	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs900735	0.83[AFR][1000 genomes]
rs9682401	0.83[AFR][1000 genomes]
rs9879397	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50655400-50677800	Weak transcription	Aorta	Aorta
2	chr3:50655600-50681200	Weak transcription	Fetal Brain Female	brain
3	chr3:50656000-50675600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50656000-50677800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:50657600-50678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:50660200-50677000	Weak transcription	Liver	Liver
7	chr3:50661600-50674400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:50661600-50675800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:50661600-50688200	Weak transcription	Small Intestine	intestine
10	chr3:50662400-50678200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:50662600-50675800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:50663200-50677600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:50665200-50674400	Weak transcription	Colonic Mucosa	Colon
15	chr3:50665400-50679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:50665400-50686800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:50665600-50673800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:50665600-50675600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:50665600-50686200	Weak transcription	Stomach Mucosa	stomach
20	chr3:50665800-50674000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:50665800-50675400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:50665800-50675600	Weak transcription	Brain Substantia Nigra	brain
23	chr3:50665800-50675800	Weak transcription	NHLF	lung
24	chr3:50666200-50673600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:50666600-50675400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:50667000-50674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:50667200-50673800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:50667200-50680400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:50668000-50673400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:50668000-50673800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:50668200-50673600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:50668600-50673600	Weak transcription	HSMM	muscle
33	chr3:50668600-50673800	Weak transcription	Fetal Kidney	kidney
34	chr3:50668600-50678800	Weak transcription	Pancreas	Pancrea
35	chr3:50668600-50679200	Weak transcription	HepG2	liver
36	chr3:50669000-50675800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:50669000-50684800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:50669200-50675800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:50669400-50673600	Weak transcription	NHDF-Ad	bronchial
40	chr3:50670200-50674200	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:50670200-50675800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:50670200-50689000	Weak transcription	K562	blood
43	chr3:50670400-50673600	Weak transcription	Osteobl	bone
44	chr3:50670400-50673800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:50670400-50674000	Weak transcription	Fetal Lung	lung
46	chr3:50670400-50675600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:50670400-50675800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:50670400-50678000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:50670400-50699800	Weak transcription	Hela-S3	cervix
50	chr3:50670600-50673200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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