Variant report

Variant	rs4008320
Chromosome Location	chr9:7024648-7024649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10758820	0.81[AMR][1000 genomes]
rs10975990	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2381535	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7027561	0.80[ASN][1000 genomes]
rs7037803	0.83[ASN][1000 genomes]
rs7041764	0.80[ASN][1000 genomes]
rs7860217	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
3	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
4	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv892187	chr9:6974101-7035727	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv949711	chr9:6994399-7045058	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv892188	chr9:6999846-7026860	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv613257	chr9:7015330-7037370	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1024763	chr9:7022554-7061314	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4008320	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:7009000-7026200	Weak transcription	A549	lung
3	chr9:7009000-7027400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:7009000-7027800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:7009000-7027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:7009000-7028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:7009000-7030400	Weak transcription	NHEK	skin
8	chr9:7009000-7044800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:7009000-7046200	Weak transcription	Small Intestine	intestine
10	chr9:7009000-7055200	Weak transcription	K562	blood
11	chr9:7009000-7056400	Weak transcription	Brain Substantia Nigra	brain
12	chr9:7009000-7076600	Weak transcription	HSMM	muscle
13	chr9:7009200-7077600	Weak transcription	Osteobl	bone
14	chr9:7009400-7029600	Weak transcription	Hela-S3	cervix
15	chr9:7009400-7042000	Weak transcription	NHDF-Ad	bronchial
16	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
17	chr9:7011800-7048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:7012200-7027400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:7012200-7027400	Weak transcription	Brain Anterior Caudate	brain
20	chr9:7012200-7027400	Weak transcription	Right Ventricle	heart
21	chr9:7012200-7027400	Weak transcription	Spleen	Spleen
22	chr9:7012200-7027600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:7012200-7046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:7012200-7052600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
26	chr9:7012400-7028000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:7012800-7027600	Weak transcription	Esophagus	oesophagus
28	chr9:7012800-7028400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:7012800-7048800	Weak transcription	Dnd41	blood
30	chr9:7012800-7076800	Weak transcription	Pancreas	Pancrea
31	chr9:7013800-7031800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr9:7014200-7027400	Weak transcription	Ovary	ovary
33	chr9:7014600-7048000	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:7016000-7025200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:7016000-7036400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:7016200-7033200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:7016800-7027600	Weak transcription	Fetal Stomach	stomach
38	chr9:7017000-7027200	Weak transcription	Aorta	Aorta
39	chr9:7017000-7027600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:7017200-7026000	Weak transcription	Fetal Intestine Small	intestine
41	chr9:7017200-7026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:7017200-7027200	Weak transcription	Gastric	stomach
43	chr9:7017200-7028200	Weak transcription	Left Ventricle	heart
44	chr9:7017200-7028400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr9:7017200-7028800	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:7017400-7027400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:7017800-7027600	Weak transcription	Thymus	Thymus
48	chr9:7017800-7075000	Weak transcription	HepG2	liver
49	chr9:7018000-7027400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:7018200-7027400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links