Variant report

Variant	rs2035511
Chromosome Location	chr4:79352460-79352461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79351128..79354681-chr4:79359469..79361827,3	K562	blood:

Variant related genes	Relation type
ENSG00000138759	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10001798	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10001918	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10018235	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10026662	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006079	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1027444	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11730871	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13106736	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1484331	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1484342	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1484343	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496581	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496582	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496583	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496584	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17003266	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2054721	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054722	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627648	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627649	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627650	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627651	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2627653	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2627654	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627655	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627656	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645143	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645144	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645145	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645146	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645147	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645148	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645149	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28522970	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28566963	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2867068	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2867070	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2903470	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34840208	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36095733	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3762844	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3899004	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4975065	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4975067	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62308116	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6816851	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753751	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753752	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674053	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7699000	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs924149	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs949507	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs959539	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2035511	PAQR3	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79284600-79353600	Weak transcription	Left Ventricle	heart
2	chr4:79302400-79353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:79318800-79353600	Weak transcription	Pancreas	Pancrea
4	chr4:79320000-79400200	Weak transcription	Psoas Muscle	Psoas
5	chr4:79329000-79362000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:79332200-79353800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:79332600-79362000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:79333200-79391000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:79335000-79355600	Weak transcription	Fetal Brain Male	brain
10	chr4:79339000-79374200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:79339200-79354200	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr4:79339400-79373000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:79339600-79354400	Weak transcription	HSMMtube	muscle
14	chr4:79339600-79360600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:79339600-79360600	Weak transcription	HMEC	breast
16	chr4:79339800-79353800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:79339800-79370400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:79339800-79370400	Weak transcription	Fetal Lung	lung
19	chr4:79339800-79374800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:79340000-79354600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:79340000-79356000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:79340000-79374200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:79340400-79353600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:79340400-79362800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:79341200-79353600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:79341800-79353800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:79341800-79372600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:79343200-79431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:79344200-79370800	Weak transcription	Fetal Heart	heart
30	chr4:79344200-79375600	Weak transcription	Fetal Stomach	stomach
31	chr4:79345600-79353600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:79346200-79353600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:79348000-79353000	Strong transcription	HepG2	liver
34	chr4:79348400-79378000	Weak transcription	Right Ventricle	heart
35	chr4:79348600-79353600	Weak transcription	Fetal Intestine Small	intestine
36	chr4:79348800-79354400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:79349600-79362000	Weak transcription	Right Atrium	heart
38	chr4:79349800-79354200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:79350000-79354000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:79350200-79353800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:79351400-79353800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:79351600-79353400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:79351600-79353600	Weak transcription	Aorta	Aorta
44	chr4:79351800-79353400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:79351800-79353800	Weak transcription	Fetal Kidney	kidney
46	chr4:79352000-79353400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:79352000-79353400	Weak transcription	Fetal Intestine Large	intestine
48	chr4:79352000-79353600	Weak transcription	H9 Cell Line	embryonic stem cell

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