Variant report

Variant	rs6438532
Chromosome Location	chr3:119199451-119199452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119185648..119192167-chr3:119194088..119200916,11	MCF-7	breast:
2	chr3:119193841..119196311-chr3:119198584..119200554,2	K562	blood:
3	chr3:119198406..119200057-chr3:119200931..119203738,2	MCF-7	breast:
4	chr3:119198506..119203042-chr3:119214279..119220146,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11712863	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11713200	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2049756	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2178318	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282171	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3195852	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35078244	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3732419	0.95[YRI][hapmap]
rs3772136	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3932422	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687859	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4688003	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6763561	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6777535	0.95[YRI][hapmap]
rs6797866	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6799691	0.95[YRI][hapmap]
rs7430156	0.80[YRI][hapmap]
rs7430798	0.95[YRI][hapmap]
rs7613562	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7629750	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9289129	0.82[YRI][hapmap]
rs9713715	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9833154	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9846088	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9851177	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9855347	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9872589	0.95[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.98[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	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6438532	POGLUT1	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119188600-119216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:119188800-119216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:119189000-119204400	Weak transcription	NHDF-Ad	bronchial
6	chr3:119189000-119216200	Weak transcription	Stomach Mucosa	stomach
7	chr3:119189000-119216200	Weak transcription	HUVEC	blood vessel
8	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:119189200-119199600	Weak transcription	HMEC	breast
10	chr3:119189200-119203000	Weak transcription	Fetal Kidney	kidney
11	chr3:119189400-119201800	Strong transcription	Fetal Stomach	stomach
12	chr3:119189600-119205400	Weak transcription	Hela-S3	cervix
13	chr3:119189600-119209200	Strong transcription	Primary B cells from cord blood	blood
14	chr3:119189600-119211800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:119189600-119211800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:119189800-119200800	Strong transcription	Fetal Thymus	thymus
17	chr3:119189800-119210000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:119189800-119211400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:119189800-119212200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:119189800-119216000	Weak transcription	Fetal Heart	heart
21	chr3:119190000-119201200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:119190000-119201800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:119190000-119202000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:119190000-119211800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:119190200-119200200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:119190400-119212200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:119190600-119204800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:119190600-119211800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:119190600-119212000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:119190800-119199800	Weak transcription	Fetal Lung	lung
33	chr3:119190800-119204200	Weak transcription	A549	lung
34	chr3:119190800-119204200	Weak transcription	HSMMtube	muscle
35	chr3:119190800-119205000	Weak transcription	Psoas Muscle	Psoas
36	chr3:119190800-119216400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:119191000-119203200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:119191000-119216400	Weak transcription	Fetal Brain Male	brain
39	chr3:119192000-119209800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:119192400-119207200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:119192400-119216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:119193800-119204600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:119194200-119205400	Weak transcription	NHLF	lung
44	chr3:119195400-119200400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:119195400-119200400	Strong transcription	Brain Anterior Caudate	brain
46	chr3:119195400-119202000	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:119195800-119201200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:119195800-119201200	Strong transcription	Dnd41	blood
49	chr3:119195800-119212000	Strong transcription	Liver	Liver
50	chr3:119196000-119199600	Strong transcription	Fetal Muscle Trunk	muscle

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