Variant report

Variant	rs6438521
Chromosome Location	chr3:119030321-119030322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119011664..119014581-chr3:119029307..119032629,3	MCF-7	breast:
2	chr3:119028893..119037158-chr3:119037697..119043591,18	MCF-7	breast:
3	chr3:119030074..119031736-chr3:119039533..119042387,2	K562	blood:

Variant related genes	Relation type
ENSG00000031081	Chromatin interaction
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934490	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12497738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13314464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1375135	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1448434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687994	0.87[EUR][1000 genomes]
rs58568360	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62265236	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62265237	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6438518	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6438519	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6438520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438522	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6438523	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762580	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785727	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6786522	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6789881	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6799733	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7610546	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7611832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619210	0.86[EUR][1000 genomes]
rs7644570	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649480	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7649930	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9822211	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9825078	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834750	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9847963	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9861372	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9861688	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9877740	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119014200-119032800	Weak transcription	Pancreas	Pancrea
2	chr3:119015000-119041200	Weak transcription	Aorta	Aorta
3	chr3:119015200-119041000	Weak transcription	Fetal Kidney	kidney
4	chr3:119016000-119035400	Weak transcription	Fetal Brain Male	brain
5	chr3:119016000-119041000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:119016400-119040800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:119016400-119041000	Weak transcription	Fetal Intestine Small	intestine
8	chr3:119017400-119040600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:119017600-119032400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:119018800-119032800	Weak transcription	Thymus	Thymus
11	chr3:119019200-119040800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:119020400-119040600	Weak transcription	Esophagus	oesophagus
13	chr3:119020800-119030400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:119020800-119032400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:119021000-119030400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:119021000-119032400	Weak transcription	Primary T cells from cord blood	blood
17	chr3:119021200-119041000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:119021200-119041000	Weak transcription	Fetal Thymus	thymus
19	chr3:119022000-119032400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:119022200-119040800	Weak transcription	Brain Angular Gyrus	brain
21	chr3:119022400-119040600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:119022400-119041000	Weak transcription	Primary B cells from cord blood	blood
23	chr3:119022400-119041000	Weak transcription	Fetal Intestine Large	intestine
24	chr3:119022400-119041200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:119022600-119032600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:119022600-119040600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:119023600-119032800	Weak transcription	Ovary	ovary
28	chr3:119024400-119040600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:119024800-119032400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:119024800-119032600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:119024800-119032800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:119024800-119040600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:119024800-119041000	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:119024800-119041000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:119025000-119040800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:119026800-119034600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:119027200-119031000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:119027600-119030600	Strong transcription	Fetal Stomach	stomach
39	chr3:119027600-119031200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:119027600-119033800	Weak transcription	Brain Substantia Nigra	brain
41	chr3:119027600-119041000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:119027800-119030800	Enhancers	Right Atrium	heart
43	chr3:119028000-119031000	Enhancers	NHDF-Ad	bronchial
44	chr3:119028000-119031000	Enhancers	NHLF	lung
45	chr3:119028000-119031200	Enhancers	HMEC	breast
46	chr3:119028200-119030600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:119028200-119030600	Enhancers	Adipose Nuclei	Adipose
48	chr3:119028200-119031000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:119028200-119031000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:119028200-119032800	Weak transcription	Fetal Muscle Leg	muscle

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