Variant report

Variant	rs62533900
Chromosome Location	chr9:7086502-7086503
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	chr9:7080307..7083078-chr9:7084798..7086869,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16925292	0.82[AMR][1000 genomes]
rs55787411	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62533862	0.80[ASN][1000 genomes]
rs62533897	0.82[AMR][1000 genomes]
rs62533899	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73639964	0.80[ASN][1000 genomes]
rs73639965	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869932	chr9:7068359-7133384	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62533900	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
2	chr9:7034000-7103600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr9:7043400-7103600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:7051600-7103200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr9:7053000-7086600	Weak transcription	Fetal Intestine Large	intestine
6	chr9:7053200-7099200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:7058400-7088600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:7061200-7104600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:7061600-7103600	Weak transcription	Spleen	Spleen
10	chr9:7062800-7096400	Weak transcription	Fetal Intestine Small	intestine
11	chr9:7066200-7096200	Weak transcription	Stomach Mucosa	stomach
12	chr9:7067000-7088000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:7067200-7103600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:7068400-7103600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:7071200-7087400	Strong transcription	Primary B cells from cord blood	blood
16	chr9:7072000-7088600	Strong transcription	Primary T cells from cord blood	blood
17	chr9:7073600-7099200	Weak transcription	NHEK	skin
18	chr9:7074600-7089800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:7075000-7097800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:7075400-7088400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:7075600-7105800	Weak transcription	NHLF	lung
22	chr9:7076600-7103600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:7077000-7098000	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:7077800-7086600	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:7077800-7089600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:7077800-7089800	Weak transcription	Psoas Muscle	Psoas
27	chr9:7077800-7103200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr9:7077800-7103200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:7077800-7103600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr9:7077800-7103600	Weak transcription	Brain Angular Gyrus	brain
31	chr9:7077800-7103600	Weak transcription	HMEC	breast
32	chr9:7077800-7103600	Weak transcription	K562	blood
33	chr9:7077800-7103800	Weak transcription	HSMM	muscle
34	chr9:7078000-7086600	Weak transcription	Left Ventricle	heart
35	chr9:7078000-7089400	Weak transcription	HSMMtube	muscle
36	chr9:7078000-7094000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:7078000-7103600	Weak transcription	Dnd41	blood
38	chr9:7078200-7103800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:7078400-7094600	Weak transcription	GM12878-XiMat	blood
40	chr9:7078600-7086600	Weak transcription	Placenta	Placenta
41	chr9:7079200-7088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:7079400-7086600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:7079400-7103200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr9:7079600-7103600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:7081600-7089800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:7081600-7090600	Weak transcription	Fetal Heart	heart
47	chr9:7081600-7097000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:7081800-7088400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr9:7082800-7103600	Weak transcription	Pancreas	Pancrea
50	chr9:7083000-7091800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links