Variant report

Variant	rs1544055
Chromosome Location	chr9:7084529-7084530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10739114	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10815511	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1093703	0.82[JPT][hapmap]
rs1093705	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10975997	0.94[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs1570509	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1570513	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2381540	0.93[CEU][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381541	0.87[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381542	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381544	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381545	0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3898792	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4523317	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4641121	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742294	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4742296	0.87[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4742298	0.81[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742300	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4742301	0.85[AMR][1000 genomes]
rs4742302	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4742305	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6477142	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6477143	0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6477144	0.94[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6477147	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6477149	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6477150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7031179	0.94[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs7852014	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs7858761	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs864696	0.84[EUR][1000 genomes]
rs866566	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv466117	chr9:7030268-7084558	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv613258	chr9:7030268-7084558	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
rs1544055	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
2	chr9:7028800-7086400	Weak transcription	Right Ventricle	heart
3	chr9:7034000-7103600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr9:7043400-7103600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:7051600-7103200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:7052600-7086400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:7053000-7086600	Weak transcription	Fetal Intestine Large	intestine
8	chr9:7053200-7099200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:7058400-7088600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:7058600-7085000	Weak transcription	Brain Anterior Caudate	brain
11	chr9:7061200-7104600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:7061600-7103600	Weak transcription	Spleen	Spleen
13	chr9:7062800-7096400	Weak transcription	Fetal Intestine Small	intestine
14	chr9:7066200-7096200	Weak transcription	Stomach Mucosa	stomach
15	chr9:7067000-7088000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:7067200-7103600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:7068400-7103600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:7071200-7087400	Strong transcription	Primary B cells from cord blood	blood
19	chr9:7072000-7088600	Strong transcription	Primary T cells from cord blood	blood
20	chr9:7073600-7099200	Weak transcription	NHEK	skin
21	chr9:7074600-7089800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:7075000-7097800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr9:7075400-7086400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:7075400-7088400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:7075600-7105800	Weak transcription	NHLF	lung
26	chr9:7076600-7103600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:7077000-7086400	Weak transcription	Hela-S3	cervix
28	chr9:7077000-7098000	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:7077200-7085000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:7077800-7086400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:7077800-7086400	Weak transcription	Aorta	Aorta
32	chr9:7077800-7086400	Weak transcription	Esophagus	oesophagus
33	chr9:7077800-7086400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:7077800-7086400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:7077800-7086600	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:7077800-7089600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:7077800-7089800	Weak transcription	Psoas Muscle	Psoas
38	chr9:7077800-7103200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr9:7077800-7103200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:7077800-7103600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:7077800-7103600	Weak transcription	Brain Angular Gyrus	brain
42	chr9:7077800-7103600	Weak transcription	HMEC	breast
43	chr9:7077800-7103600	Weak transcription	K562	blood
44	chr9:7077800-7103800	Weak transcription	HSMM	muscle
45	chr9:7078000-7086200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:7078000-7086400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:7078000-7086400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr9:7078000-7086400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr9:7078000-7086400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr9:7078000-7086400	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links