Variant report

Variant	rs248218
Chromosome Location	chr5:179311942-179311943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179305874..179308839-chr5:179309473..179313731,6	MCF-7	breast:
2	chr5:179286272..179289158-chr5:179311658..179315263,3	K562	blood:
3	chr5:179309888..179313402-chr5:179319513..179322081,3	MCF-7	breast:
4	chr5:179310913..179313966-chr5:179318977..179321950,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs155796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs182086	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[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2431124	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[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248217	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs248219	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248220	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[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26074	0.93[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26075	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs26077	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26078	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27410	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[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	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30382	0.94[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]
rs32437	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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[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	0.93[CHB][hapmap];0.91[JPT][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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[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[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574997	1.00[CHB][hapmap];1.00[JPT][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]
rs88183	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]
rs9957	0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs248218	SQSTM1	Cis_1M	lymphoblastoid	RTeQTL
rs248218	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	chr5:179309200-179312000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
6	chr5:179309200-179312000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr5:179309200-179312000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:179309200-179312000	ZNF genes & repeats	Fetal Brain Female	brain
9	chr5:179309200-179312200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:179309200-179312200	ZNF genes & repeats	Fetal Muscle Leg	muscle
11	chr5:179309200-179312400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr5:179309200-179312400	ZNF genes & repeats	Fetal Lung	lung
13	chr5:179309200-179312800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179309200-179312800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:179309200-179313600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:179309200-179313800	ZNF genes & repeats	A549	lung
17	chr5:179309200-179313800	ZNF genes & repeats	Dnd41	blood
18	chr5:179309200-179314400	ZNF genes & repeats	GM12878-XiMat	blood
19	chr5:179309200-179327200	Strong transcription	Brain Angular Gyrus	brain
20	chr5:179309400-179312000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:179309400-179312000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
22	chr5:179309400-179312000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:179309400-179312000	ZNF genes & repeats	NHDF-Ad	bronchial
24	chr5:179309400-179312200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:179309400-179312200	ZNF genes & repeats	HMEC	breast
26	chr5:179309400-179312400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr5:179309400-179313000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:179309400-179313000	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr5:179309400-179313200	ZNF genes & repeats	Fetal Stomach	stomach
30	chr5:179309400-179313400	ZNF genes & repeats	NHEK	skin
31	chr5:179309400-179313600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:179309600-179312000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr5:179309600-179312200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:179309600-179312200	ZNF genes & repeats	K562	blood
35	chr5:179309600-179312600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:179309600-179312800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:179309800-179312000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
38	chr5:179309800-179312200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
39	chr5:179309800-179312200	ZNF genes & repeats	Primary B cells from cord blood	blood
40	chr5:179309800-179326400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:179310000-179312200	ZNF genes & repeats	Fetal Heart	heart
42	chr5:179310000-179312800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:179310200-179327400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr5:179310400-179323200	Strong transcription	Gastric	stomach
45	chr5:179310400-179326800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:179310400-179332000	Strong transcription	Fetal Intestine Large	intestine
47	chr5:179310600-179312200	Strong transcription	Pancreatic Islets	Pancreatic Islet
48	chr5:179310600-179312200	ZNF genes & repeats	NHLF	lung
49	chr5:179310600-179314800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr5:179310600-179314800	Strong transcription	Hela-S3	cervix

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