Variant report

Variant	rs62489381
Chromosome Location	chr7:129588250-129588251
allele	A/G
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	TEAD4	chr7:129588095-129589857	ECC-1	luminal epithelium:	n/a	chr7:129589276-129589285
2	CBX3	chr7:129588149-129589225	K562	blood:	n/a	n/a
3	POLR2A	chr7:129588016-129593036	SK-N-SH	brain:	n/a	n/a
4	JUND	chr7:129586819-129593622	SK-N-SH	brain:	n/a	chr7:129589371-129589383 chr7:129589371-129589382 chr7:129592822-129592831 chr7:129592808-129592817 chr7:129589107-129589118 chr7:129588334-129588342 chr7:129588333-129588343 chr7:129588333-129588343 chr7:129589373-129589381
5	PBX3	chr7:129588021-129589954	SK-N-SH	brain:	n/a	n/a
6	EP300	chr7:129587451-129593634	SK-N-SH	brain:	n/a	chr7:129588688-129588702 chr7:129592865-129592874 chr7:129589432-129589445 chr7:129591093-129591107 chr7:129592906-129592920 chr7:129587603-129587617 chr7:129587516-129587526 chr7:129589989-129589998 chr7:129590804-129590817 chr7:129592472-129592481
7	POLR2A	chr7:129588214-129588455	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:129586771-129588387	K562	blood:	n/a	n/a
9	RFX5	chr7:129588156-129589662	IMR90	lung:	n/a	chr7:129589159-129589168 chr7:129589157-129589173 chr7:129589156-129589170
10	RFX5	chr7:129586524-129593512	SK-N-SH	brain:	n/a	chr7:129589159-129589168 chr7:129589157-129589173 chr7:129589156-129589170
11	POLR2A	chr7:129588134-129592912	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:129587456..129589237-chr7:129595459..129597613,2	K562	blood:
2	chr7:129470865..129472484-chr7:129587803..129590371,2	K562	blood:
3	chr7:129577601..129579299-chr7:129587764..129589534,2	MCF-7	breast:
4	chr7:129575738..129578941-chr7:129585169..129588929,4	K562	blood:
5	chr7:129469886..129472381-chr7:129587283..129590699,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244036	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10215972	0.83[ASN][1000 genomes]
rs12533468	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34297290	0.82[ASN][1000 genomes]
rs3807121	0.87[ASN][1000 genomes]
rs3817530	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4728180	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4731638	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56222328	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62489376	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62489377	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62489378	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62489379	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62489382	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62491533	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62491539	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	nsv533849	chr7:129462947-129616625	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv831129	chr7:129525406-129702477	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129559800-129588600	Weak transcription	Colonic Mucosa	Colon
2	chr7:129574000-129588600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr7:129577800-129589600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:129579400-129588400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:129580600-129588600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:129582000-129589000	Weak transcription	Ovary	ovary
7	chr7:129582000-129589600	Weak transcription	Lung	lung
8	chr7:129584600-129588400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:129584600-129588600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:129584800-129588800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:129586200-129588400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:129586200-129588400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr7:129586200-129588600	Enhancers	HepG2	liver
14	chr7:129586200-129588800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:129586400-129588600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:129586400-129588800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr7:129586400-129588800	Enhancers	Brain Cingulate Gyrus	brain
18	chr7:129586400-129590400	Enhancers	Small Intestine	intestine
19	chr7:129586600-129588400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr7:129586600-129588600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr7:129586600-129588600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr7:129586600-129588800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr7:129586600-129588800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:129586600-129589000	Enhancers	Fetal Heart	heart
25	chr7:129586800-129588600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr7:129586800-129588600	Enhancers	Brain Anterior Caudate	brain
27	chr7:129586800-129588600	Enhancers	Fetal Kidney	kidney
28	chr7:129586800-129588600	Enhancers	Osteobl	bone
29	chr7:129586800-129588800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr7:129587000-129588400	Enhancers	Primary T cells from cord blood	blood
31	chr7:129587000-129588400	Enhancers	Brain Hippocampus Middle	brain
32	chr7:129587000-129588600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr7:129587000-129588600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr7:129587000-129588600	Enhancers	Adipose Nuclei	Adipose
35	chr7:129587000-129588600	Enhancers	NH-A	brain
36	chr7:129587000-129588800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:129587000-129588800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr7:129587000-129588800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr7:129587000-129588800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr7:129587000-129588800	Enhancers	Fetal Lung	lung
41	chr7:129587000-129588800	Enhancers	Left Ventricle	heart
42	chr7:129587000-129589000	Enhancers	Right Ventricle	heart
43	chr7:129587200-129588400	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr7:129587200-129588600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:129587200-129588600	Enhancers	HSMM	muscle
46	chr7:129587200-129588800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:129587200-129588800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:129587200-129588800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:129587200-129588800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr7:129587400-129588400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links