Variant report

Variant	rs12533084
Chromosome Location	chr7:21932876-21932877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11773744	0.86[CEU][hapmap]
rs12533111	0.86[JPT][hapmap]
rs12534688	0.81[ASN][1000 genomes]
rs12537531	0.91[JPT][hapmap]
rs12700317	0.90[CEU][hapmap]
rs4484586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60626359	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61114344	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62445896	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62445897	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62445900	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62445901	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73077549	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9639401	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs9639402	0.81[CHB][hapmap];0.85[JPT][hapmap]

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	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12533084	IL6	cis	cerebellum	SCAN
rs12533084	CDCA7L	cis	lymphoblastoid	seeQTL
rs12533084	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21907400-21937200	Weak transcription	Fetal Thymus	thymus
2	chr7:21908400-21936600	Weak transcription	Primary T cells from cord blood	blood
3	chr7:21910000-21939400	Weak transcription	Left Ventricle	heart
4	chr7:21911200-21938400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:21916400-21933800	Weak transcription	Thymus	Thymus
6	chr7:21916800-21935000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:21916800-21936600	Weak transcription	Primary B cells from cord blood	blood
8	chr7:21917000-21936600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:21917000-21938400	Weak transcription	Fetal Intestine Small	intestine
10	chr7:21923000-21937800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:21923200-21938600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:21924000-21937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:21924400-21937800	Weak transcription	NHEK	skin
14	chr7:21924400-21945400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:21924800-21936400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:21926400-21937800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:21926600-21942600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:21926800-21933800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:21926800-21937000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:21926800-21938000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:21926800-21939200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:21927800-21936600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:21927800-21937600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:21927800-21937800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:21927800-21938400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr7:21927800-21940200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:21928000-21934000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:21928000-21936600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:21928000-21937200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr7:21928000-21942600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:21928200-21937600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr7:21928200-21938600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:21928200-21939600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:21928800-21938400	Weak transcription	NHDF-Ad	bronchial
35	chr7:21929200-21938000	Weak transcription	Fetal Lung	lung
36	chr7:21929600-21936400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:21929800-21938000	Weak transcription	Right Ventricle	heart
38	chr7:21930000-21937800	Weak transcription	Gastric	stomach
39	chr7:21930400-21937600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:21930800-21938400	Weak transcription	Esophagus	oesophagus
41	chr7:21931000-21942400	Weak transcription	Fetal Kidney	kidney
42	chr7:21931200-21934800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:21931400-21937800	Weak transcription	Fetal Stomach	stomach
44	chr7:21932200-21937000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:21932600-21937800	Weak transcription	Fetal Heart	heart
46	chr7:21932600-21938000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:21932600-21938200	Weak transcription	Hela-S3	cervix
48	chr7:21932600-21938400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:21932600-21938400	Weak transcription	Brain Anterior Caudate	brain
50	chr7:21932600-21942000	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links