Variant report

Variant	rs1183319
Chromosome Location	chr3:178969107-178969108
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	chr3:178961023..178967533-chr3:178968774..178973213,9	K562	blood:

Variant related genes	Relation type
ENSG00000171121	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1059691	0.81[ASN][1000 genomes]
rs1170673	0.86[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11706842	0.86[CHD][hapmap]
rs1180368	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11919383	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs11922631	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12488074	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs3729674	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs3729676	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs4080957	0.81[ASN][1000 genomes]
rs4855093	0.86[CHD][hapmap]
rs56095736	0.81[ASN][1000 genomes]
rs59408989	0.81[ASN][1000 genomes]
rs6443619	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6443624	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6443628	0.81[ASN][1000 genomes]
rs6443629	0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs67562832	0.81[ASN][1000 genomes]
rs6769154	0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6769162	0.81[ASN][1000 genomes]
rs6771313	0.81[ASN][1000 genomes]
rs6782557	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6786049	0.86[CHD][hapmap]
rs6786114	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6798817	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6799756	0.86[CHD][hapmap]
rs6806917	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs6810246	0.86[CHD][hapmap]
rs7372645	0.81[ASN][1000 genomes]
rs7614305	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7615076	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7621329	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7621436	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7636454	0.86[CHD][hapmap]
rs7641889	0.85[CHD][hapmap]
rs7641983	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7644648	0.86[JPT][hapmap]
rs7645550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.94[ASN][1000 genomes]
rs7646409	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7651265	0.86[CHD][hapmap]
rs9813190	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9817020	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9829903	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9831234	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs9833438	0.81[ASN][1000 genomes]
rs9838411	0.86[CHD][hapmap]
rs9844270	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9844482	0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9866361	0.86[JPT][hapmap]

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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	esv1800747	chr3:178962897-178977074	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
11	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1183319	CLCN2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
2	chr3:178914800-178972800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:178932200-178974000	Weak transcription	Lung	lung
4	chr3:178941800-178972600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:178945800-178978400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:178948800-178978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:178949000-178970800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:178949000-178978200	Weak transcription	NHLF	lung
9	chr3:178949000-178978600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:178949000-178978600	Weak transcription	Ovary	ovary
11	chr3:178949000-178978800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:178949200-178978400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:178949200-178978600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:178949200-178978600	Weak transcription	Osteobl	bone
15	chr3:178952000-178978400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:178952200-178970400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:178952200-178973000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:178952400-178971200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:178952400-178971400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:178952400-178978600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:178952600-178976600	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:178954600-178970800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:178954600-178972400	Weak transcription	Fetal Intestine Small	intestine
24	chr3:178955000-178973800	Weak transcription	HSMMtube	muscle
25	chr3:178955200-178974400	Weak transcription	GM12878-XiMat	blood
26	chr3:178955400-178970600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:178956200-178977000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:178959800-178978800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:178963200-178970000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:178963200-178970600	Weak transcription	Placenta	Placenta
31	chr3:178963200-178971000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:178963200-178978200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:178963200-178978600	Weak transcription	Left Ventricle	heart
34	chr3:178963200-178978800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:178963800-178978800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:178965400-178970000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:178966000-178971400	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:178966200-178978600	Weak transcription	HUVEC	blood vessel
39	chr3:178967200-178969400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:178967200-178969400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:178967400-178969200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:178967400-178969400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:178967400-178969600	Strong transcription	Aorta	Aorta
44	chr3:178967600-178969200	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:178967800-178969400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:178968000-178970400	Strong transcription	K562	blood
47	chr3:178968400-178969600	Flanking Active TSS	HepG2	liver
48	chr3:178968600-178969200	Enhancers	A549	lung
49	chr3:178968600-178969400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:178968600-178969400	Flanking Active TSS	Liver	Liver

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