Variant report

Variant	rs295299
Chromosome Location	chr3:141338068-141338069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141337365..141343869-chr3:141344227..141348794,9	K562	blood:
2	chr3:141336924..141339116-chr3:141456806..141458556,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11711375	0.88[JPT][hapmap]
rs11917587	0.88[JPT][hapmap]
rs1493209	0.88[JPT][hapmap]
rs1493210	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851438	0.83[JPT][hapmap]
rs16851441	1.00[JPT][hapmap]
rs16851483	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1863867	0.88[JPT][hapmap]
rs2035935	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2035936	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312193	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2639997	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295300	0.88[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs295320	0.88[JPT][hapmap]
rs295321	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295323	0.88[JPT][hapmap]
rs295324	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34558081	0.93[ASN][1000 genomes]
rs3732869	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806646	0.88[JPT][hapmap]
rs3806648	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3821709	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821710	0.88[JPT][hapmap]
rs3821712	0.88[JPT][hapmap]
rs4683404	0.88[JPT][hapmap]
rs4683610	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683612	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58025624	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60654199	0.82[ASN][1000 genomes]
rs61750362	0.93[AFR][1000 genomes]
rs6767158	0.88[JPT][hapmap]
rs6785874	0.88[JPT][hapmap]
rs6795168	0.88[JPT][hapmap]
rs6800122	0.88[JPT][hapmap]
rs6808837	0.88[JPT][hapmap]
rs73871847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618787	0.90[ASW][hapmap];0.86[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs7626871	0.88[JPT][hapmap]
rs7627774	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7627807	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7643837	0.88[JPT][hapmap]
rs9878347	0.83[JPT][hapmap]
rs9879503	0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	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
rs295299	ZBTB38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:141313200-141344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:141321800-141342600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:141330000-141338800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:141330200-141338200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:141330400-141342000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:141330400-141342000	Weak transcription	Pancreas	Pancrea
8	chr3:141330400-141343200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:141330400-141344000	Weak transcription	HMEC	breast
10	chr3:141330400-141344600	Weak transcription	NHLF	lung
11	chr3:141330600-141338200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:141330600-141339000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:141330600-141339200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:141330600-141344200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:141330600-141344200	Weak transcription	Ovary	ovary
16	chr3:141330800-141338400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:141330800-141338400	Weak transcription	Left Ventricle	heart
18	chr3:141330800-141344200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:141331600-141338800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:141331800-141338600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:141332000-141344600	Weak transcription	NHDF-Ad	bronchial
22	chr3:141332200-141338200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:141332200-141339200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:141332400-141339200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:141332400-141340600	Weak transcription	A549	lung
26	chr3:141332400-141344200	Weak transcription	HSMM	muscle
27	chr3:141332400-141344400	Weak transcription	Osteobl	bone
28	chr3:141332400-141345800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:141333600-141344200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:141334000-141339000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:141334400-141338400	Strong transcription	Primary T cells from cord blood	blood
32	chr3:141335200-141344200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:141335200-141344200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:141335400-141338400	Weak transcription	Adipose Nuclei	Adipose
35	chr3:141335400-141338600	Weak transcription	Dnd41	blood
36	chr3:141335600-141338200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:141335600-141341600	Weak transcription	NH-A	brain
38	chr3:141335800-141339200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:141336000-141338200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:141336000-141338800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr3:141336000-141339600	Enhancers	Fetal Intestine Large	intestine
42	chr3:141336000-141344200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:141336200-141338400	Weak transcription	Fetal Thymus	thymus
44	chr3:141336200-141340600	Weak transcription	Fetal Stomach	stomach
45	chr3:141336200-141343800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:141336400-141339600	Enhancers	Fetal Intestine Small	intestine
47	chr3:141336600-141338200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:141336600-141338400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:141336600-141338400	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:141336800-141338400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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