Variant report

Variant	rs248217
Chromosome Location	chr5:179310330-179310331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs152233	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	0.83[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];0.83[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];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs155797	0.81[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];0.85[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]
rs248218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[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];0.98[AFR][1000 genomes];0.98[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];0.81[AMR][1000 genomes];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];0.83[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];0.95[AFR][1000 genomes];0.98[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	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30381	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30382	0.98[AFR][1000 genomes];0.98[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];0.94[AFR][1000 genomes];0.98[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	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs32472	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];0.98[AFR][1000 genomes];0.98[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]
rs88183	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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:10 , 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	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
rs248217	SQSTM1	Cis_1M	lymphoblastoid	RTeQTL
rs248217	TBC1D9B	cis	Muscle Skeletal	GTEx
rs248217	C5orf45	cis	cerebellum	SCAN
rs248217	BTNL9	cis	cerebellum	SCAN
rs248217	SLC34A1	cis	parietal	SCAN
rs248217	HIGD2A	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179286200-179310600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179286600-179310600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr5:179286600-179310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:179286600-179311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:179287200-179333600	Weak transcription	Right Atrium	heart
6	chr5:179288400-179310600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:179289600-179328000	Strong transcription	Adipose Nuclei	Adipose
8	chr5:179295200-179334000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:179302200-179310600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:179302400-179310800	Weak transcription	Psoas Muscle	Psoas
11	chr5:179304600-179310600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr5:179305200-179310600	Weak transcription	HSMMtube	muscle
13	chr5:179305800-179310600	Weak transcription	Hela-S3	cervix
14	chr5:179306800-179310800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:179306800-179311600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:179307000-179310600	Weak transcription	Brain Substantia Nigra	brain
17	chr5:179307000-179310600	Weak transcription	Left Ventricle	heart
18	chr5:179307400-179310400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:179307600-179310800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:179307600-179310800	Weak transcription	Aorta	Aorta
21	chr5:179307800-179310600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr5:179308000-179310600	Weak transcription	Colonic Mucosa	Colon
23	chr5:179308200-179310600	Weak transcription	NHLF	lung
24	chr5:179308400-179310800	Weak transcription	Right Ventricle	heart
25	chr5:179308400-179318600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:179308600-179310800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:179309200-179310800	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr5:179309200-179311400	ZNF genes & repeats	Fetal Thymus	thymus
29	chr5:179309200-179311600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
30	chr5:179309200-179311600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr5:179309200-179311600	ZNF genes & repeats	Brain Germinal Matrix	brain
32	chr5:179309200-179311800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
33	chr5:179309200-179311800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:179309200-179312000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
35	chr5:179309200-179312000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr5:179309200-179312000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:179309200-179312000	ZNF genes & repeats	Fetal Brain Female	brain
38	chr5:179309200-179312200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:179309200-179312200	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr5:179309200-179312400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
41	chr5:179309200-179312400	ZNF genes & repeats	Fetal Lung	lung
42	chr5:179309200-179312800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:179309200-179312800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:179309200-179313600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:179309200-179313800	ZNF genes & repeats	A549	lung
46	chr5:179309200-179313800	ZNF genes & repeats	Dnd41	blood
47	chr5:179309200-179314400	ZNF genes & repeats	GM12878-XiMat	blood
48	chr5:179309200-179327200	Strong transcription	Brain Angular Gyrus	brain
49	chr5:179309400-179310600	ZNF genes & repeats	Brain Anterior Caudate	brain
50	chr5:179309400-179310800	Strong transcription	Osteobl	bone

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