Variant report

Variant	rs88183
Chromosome Location	chr5:179313656-179313657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179312827..179319105-chr5:179330918..179335028,6	MCF-7	breast:
2	chr5:179305874..179308839-chr5:179309473..179313731,6	MCF-7	breast:
3	chr5:179286272..179289158-chr5:179311658..179315263,3	K562	blood:
4	chr5:179312285..179314343-chr5:179315369..179317861,2	K562	blood:
5	chr5:179310913..179313966-chr5:179318977..179321950,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs152233	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152236	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs152237	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs152238	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs155791	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs155795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs155796	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs155797	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs156101	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs156104	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1684973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs182086	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2431123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2431124	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2434411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs248218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248220	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs248222	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs248232	0.83[ASN][1000 genomes]
rs248252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26074	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26075	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs26077	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26078	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27471	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs27474	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28325	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30381	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30382	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30385	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30386	0.87[CHD][hapmap];0.91[MEX][hapmap]
rs32437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32461	0.92[ASN][1000 genomes]
rs32469	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs32470	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs32471	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs32472	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3734003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs43155	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs532795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs578659	0.83[EUR][1000 genomes]
rs860706	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9957	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][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	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
3	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
4	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
6	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers 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 miRNA target site	189 gene(s)	inside rSNPs	diseases
7	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	175 gene(s)	inside rSNPs	diseases
8	nsv883286	chr5:179290845-179313656	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs88183	C5orf45	cis	cerebellum	SCAN
rs88183	BTNL9	cis	cerebellum	SCAN
rs88183	SLC34A1	cis	parietal	SCAN
rs88183	HIGD2A	cis	cerebellum	SCAN
rs88183	SQSTM1	Cis_1M	lymphoblastoid	RTeQTL
rs88183	TBC1D9B	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179287200-179333600	Weak transcription	Right Atrium	heart
2	chr5:179289600-179328000	Strong transcription	Adipose Nuclei	Adipose
3	chr5:179295200-179334000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:179308400-179318600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:179309200-179313800	ZNF genes & repeats	A549	lung
6	chr5:179309200-179313800	ZNF genes & repeats	Dnd41	blood
7	chr5:179309200-179314400	ZNF genes & repeats	GM12878-XiMat	blood
8	chr5:179309200-179327200	Strong transcription	Brain Angular Gyrus	brain
9	chr5:179309800-179326400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:179310200-179327400	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr5:179310400-179323200	Strong transcription	Gastric	stomach
12	chr5:179310400-179326800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:179310400-179332000	Strong transcription	Fetal Intestine Large	intestine
14	chr5:179310600-179314800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:179310600-179314800	Strong transcription	Hela-S3	cervix
16	chr5:179310600-179323000	Strong transcription	Colonic Mucosa	Colon
17	chr5:179310600-179323200	Strong transcription	Brain Anterior Caudate	brain
18	chr5:179310600-179326800	Strong transcription	Brain Substantia Nigra	brain
19	chr5:179310600-179327400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr5:179310800-179314000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
21	chr5:179310800-179322800	Strong transcription	Right Ventricle	heart
22	chr5:179310800-179323200	Strong transcription	Ovary	ovary
23	chr5:179310800-179323200	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr5:179310800-179327200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:179310800-179331400	Strong transcription	Primary T cells from cord blood	blood
26	chr5:179311000-179315200	Strong transcription	NH-A	brain
27	chr5:179311000-179315400	Strong transcription	HSMM	muscle
28	chr5:179311000-179317600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:179311000-179317600	Weak transcription	Small Intestine	intestine
30	chr5:179311000-179321800	Strong transcription	Liver	Liver
31	chr5:179311000-179325000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:179311000-179326800	Strong transcription	Brain Cingulate Gyrus	brain
33	chr5:179311000-179326800	Strong transcription	Brain Hippocampus Middle	brain
34	chr5:179311000-179328200	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr5:179311000-179332000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr5:179311000-179332600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:179311200-179328200	Strong transcription	Osteobl	bone
38	chr5:179311200-179332000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:179311200-179332000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:179311400-179313800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:179311400-179317800	Strong transcription	Lung	lung
42	chr5:179311400-179322800	Strong transcription	Aorta	Aorta
43	chr5:179311400-179323000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:179311400-179323000	Strong transcription	Pancreas	Pancrea
45	chr5:179311400-179323400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:179311400-179323600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:179311400-179327400	Strong transcription	Fetal Thymus	thymus
48	chr5:179311400-179332000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr5:179311400-179332400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr5:179311400-179333800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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