Variant report

Variant	rs3195852
Chromosome Location	chr3:119157615-119157616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119157199-119157784	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:119157456-119157877	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119155062..119157702-chr3:119181053..119182622,2	MCF-7	breast:
2	chr3:119153754..119155960-chr3:119156052..119158543,2	MCF-7	breast:

Variant related genes	Relation type
TMEM39A	TF binding region
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11712863	0.81[EUR][1000 genomes]
rs11713200	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2049756	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2178318	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35078244	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3772136	0.96[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3932422	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4687859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688003	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438532	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6763561	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6797866	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7430156	0.81[AFR][1000 genomes]
rs7613562	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7629750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9713715	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9846088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9851177	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9855347	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9872589	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3195852	POGLUT1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119147000-119179000	Strong transcription	Osteobl	bone
2	chr3:119147200-119180400	Weak transcription	Stomach Mucosa	stomach
3	chr3:119147400-119179200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:119147800-119159400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:119148000-119162200	Strong transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:119148800-119157800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:119148800-119157800	Strong transcription	Stomach Smooth Muscle	stomach
8	chr3:119148800-119175400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:119148800-119180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:119149200-119159200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:119149200-119161600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:119149400-119179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:119149400-119181000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:119149400-119181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:119149600-119172600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:119150000-119162000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:119150200-119157800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:119150200-119179000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:119150400-119157800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:119150400-119159600	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:119150400-119160600	Strong transcription	Liver	Liver
22	chr3:119150400-119160800	Strong transcription	GM12878-XiMat	blood
23	chr3:119150400-119180200	Strong transcription	Fetal Intestine Large	intestine
24	chr3:119150600-119157800	Strong transcription	Primary T cells from cord blood	blood
25	chr3:119150600-119157800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:119150600-119160200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:119150600-119175400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:119150600-119180800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:119151000-119159400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:119151000-119159600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:119151000-119160800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:119151000-119165000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:119152000-119178000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:119152000-119179800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:119152200-119157800	Strong transcription	Ovary	ovary
36	chr3:119152200-119178800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:119152200-119179400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:119152800-119157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:119152800-119161800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:119154000-119181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:119154400-119171400	Strong transcription	Fetal Stomach	stomach
42	chr3:119155200-119157800	Strong transcription	K562	blood
43	chr3:119155600-119159200	Strong transcription	Fetal Intestine Small	intestine
44	chr3:119156000-119164200	Weak transcription	Psoas Muscle	Psoas
45	chr3:119156200-119158800	Weak transcription	Esophagus	oesophagus
46	chr3:119156200-119163800	Weak transcription	Small Intestine	intestine
47	chr3:119156400-119165400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:119156600-119160200	Weak transcription	Right Ventricle	heart
49	chr3:119156800-119160000	Weak transcription	Fetal Heart	heart
50	chr3:119156800-119160200	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links