Variant report

Variant	rs16830730
Chromosome Location	chr3:119828512-119828513
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	chr3:119812621..119817617-chr3:119824950..119830930,7	K562	blood:
2	chr3:119817451..119819097-chr3:119825949..119828864,2	K562	blood:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10433404	1.00[CEU][hapmap]
rs10934502	0.82[CEU][hapmap]
rs10934503	0.82[CEU][hapmap]
rs10934505	0.82[CEU][hapmap]
rs10934506	0.82[CEU][hapmap]
rs11915717	0.82[CEU][hapmap]
rs12053912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12634476	0.82[CEU][hapmap]
rs12638973	0.82[CEU][hapmap]
rs1488766	0.95[ASN][1000 genomes]
rs1870931	0.82[CEU][hapmap]
rs334541	0.95[JPT][hapmap]
rs334543	0.95[JPT][hapmap]
rs4688046	0.82[CEU][hapmap]
rs4688047	0.82[CEU][hapmap]
rs4688054	0.82[CEU][hapmap]
rs6804929	0.81[MKK][hapmap]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
6	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16830730	IQCB1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119814600-119830600	Weak transcription	Gastric	stomach
2	chr3:119815000-119829200	Weak transcription	Ovary	ovary
3	chr3:119815400-119828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:119815400-119830000	Weak transcription	Fetal Lung	lung
5	chr3:119815800-119829000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:119816000-119828600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:119816000-119829000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:119816200-119831000	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:119816200-119832600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:119816400-119831400	Weak transcription	Brain Substantia Nigra	brain
11	chr3:119818000-119831800	Weak transcription	HSMM	muscle
12	chr3:119818200-119828600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:119818600-119831800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:119819000-119828600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:119819800-119832400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:119820000-119832200	Weak transcription	HSMMtube	muscle
17	chr3:119820200-119832000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:119820600-119829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:119821400-119832000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:119822000-119829400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:119822000-119830200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:119822000-119831800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:119822000-119835200	Weak transcription	Psoas Muscle	Psoas
24	chr3:119822200-119829800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:119822200-119830600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:119822200-119830800	Weak transcription	Pancreas	Pancrea
27	chr3:119822200-119831000	Weak transcription	Esophagus	oesophagus
28	chr3:119822400-119830600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:119822400-119831800	Weak transcription	Liver	Liver
30	chr3:119822600-119829600	Weak transcription	Fetal Brain Male	brain
31	chr3:119822600-119831800	Weak transcription	A549	lung
32	chr3:119825200-119829400	Weak transcription	NHEK	skin
33	chr3:119825200-119829800	Weak transcription	Placenta	Placenta
34	chr3:119826000-119829400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:119827600-119829400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:119827800-119829200	Weak transcription	Fetal Thymus	thymus
37	chr3:119827800-119829400	Weak transcription	HMEC	breast
38	chr3:119828200-119828600	Enhancers	NHDF-Ad	bronchial
39	chr3:119828400-119834600	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links