Variant report

Variant	rs1042658
Chromosome Location	chr17:38173902-38173903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38173721-38174772	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:38173011-38174885	K562	blood:	n/a	n/a
3	POLR2A	chr17:38173867-38174019	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:38173369-38174229	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr17:38173672-38174318	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr17:38173574-38174006	HUVEC	blood vessel:	n/a	n/a
7	ZNF263	chr17:38173836-38174581	HEK293-T-REx	kidney:	n/a	chr17:38174157-38174178
8	POLR2A	chr17:38170916-38176213	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr17:38170766-38176716	U87	brain:	n/a	n/a
10	POLR2A	chr17:38170628-38176722	U87	brain:	n/a	n/a
11	POLR2A	chr17:38171303-38175657	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr17:38173854-38176132	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr17:38173296-38175247	K562	blood:	n/a	n/a
14	POLR2A	chr17:38173842-38173967	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr17:38173844-38174714	HepG2	liver:	n/a	n/a
16	POLR2A	chr17:38171205-38176070	U87	brain:	n/a	n/a
17	POLR2A	chr17:38173792-38174160	GM12878	blood:	n/a	n/a
18	POLR2A	chr17:38173594-38174081	K562	blood:	n/a	n/a
19	POLR2A	chr17:38173172-38174674	Hela-S3	cervix:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38173133..38174723-chr17:38181069..38183425,2	K562	blood:
2	chr17:38171795..38174739-chr17:38253717..38256695,2	K562	blood:
3	chr17:38172520..38175725-chr17:38187607..38191443,4	MCF-7	breast:
4	chr17:38169328..38171805-chr17:38172299..38175519,5	K562	blood:
5	chr17:38172859..38176802-chr17:38178682..38181500,4	K562	blood:
6	chr17:38141745..38144493-chr17:38173834..38176591,2	MCF-7	breast:
7	chr17:38173047..38175621-chr17:38177692..38179979,3	MCF-7	breast:
8	chr17:38171100..38173173-chr17:38173231..38176436,3	K562	blood:
9	chr17:38171930..38174052-chr17:38295398..38298227,2	MCF-7	breast:
10	chr17:38143597..38146360-chr17:38172431..38175405,3	K562	blood:
11	chr17:38172636..38175341-chr17:38255721..38258482,3	MCF-7	breast:
12	chr17:38172905..38174715-chr17:38255635..38257887,2	MCF-7	breast:
13	chr17:38169328..38171032-chr17:38172943..38175519,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265799	TF binding region
ENSG00000108344	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000265799	Chromatin interaction
ENSG00000108342	Chromatin interaction
ENSG00000108349	Chromatin interaction
ENSG00000008838	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1045929	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078934	0.93[ASW][hapmap];0.84[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11655264	0.92[YRI][hapmap]
rs11658328	0.89[YRI][hapmap]
rs11871747	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12600856	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12602172	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12941811	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12950335	0.84[ASN][1000 genomes]
rs2227315	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227336	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241245	0.89[YRI][hapmap]
rs2305482	0.89[YRI][hapmap]
rs3213762	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826331	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3884477	0.86[ASN][1000 genomes]
rs3935280	0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3936197	0.86[ASN][1000 genomes]
rs4065321	0.89[YRI][hapmap]
rs4794822	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4794823	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794824	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795412	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4795414	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4795415	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4795416	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4795418	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4795419	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4795420	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55771023	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55846942	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56922390	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57065891	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57968500	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59925331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60082402	0.96[EUR][1000 genomes]
rs62065177	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6503530	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6503533	0.83[ASN][1000 genomes]
rs7021	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs709591	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]
rs709592	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];1.00[MKK][hapmap];1.00[TSI][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]
rs7208815	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7209755	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221894	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7222039	0.85[ASN][1000 genomes]
rs7502514	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7502912	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7503555	0.84[ASN][1000 genomes]
rs8065443	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs8065519	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8066582	0.89[YRI][hapmap]
rs8066846	0.84[ASN][1000 genomes]
rs8067817	0.85[ASN][1000 genomes]
rs8068260	0.81[ASN][1000 genomes]
rs8070454	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8072548	0.85[ASN][1000 genomes]
rs8073254	0.88[YRI][hapmap]
rs8075668	0.85[YRI][hapmap]
rs8078692	0.84[ASN][1000 genomes]
rs8078723	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8081692	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs868150	0.82[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9303283	0.93[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs9303284	0.87[ASN][1000 genomes]
rs9915252	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1042658	GSDMB	cis	cerebellum	SCAN
rs1042658	MED24	cis	Thyroid	GTEx
rs1042658	PCGF2	cis	cerebellum	SCAN
rs1042658	GSDMA	cis	Artery Aorta	GTEx
rs1042658	MED24	cis	parietal	SCAN
rs1042658	GSDMA	cis	lung	GTEx
rs1042658	MED24	cis	Artery Aorta	GTEx
rs1042658	MED24	cis	Artery Tibial	GTEx
rs1042658	GSDMA	cis	Esophagus Muscularis	GTEx
rs1042658	GSDMA	cis	Nerve Tibial	GTEx
rs1042658	MED24	cis	Nerve Tibial	GTEx
rs1042658	GSDMA	cis	Adipose Subcutaneous	GTEx
rs1042658	MED24	cis	cerebellum	SCAN
rs1042658	PSMD3	cis	Frontal Cortex	GTEx
rs1042658	PSMD3	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38155000-38174000	Weak transcription	Fetal Brain Female	brain
2	chr17:38166800-38174600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:38167000-38174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:38169600-38175000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr17:38169800-38175600	Enhancers	Fetal Lung	lung
9	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:38170000-38174000	Weak transcription	Brain Germinal Matrix	brain
11	chr17:38170000-38174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:38170000-38174600	Enhancers	Fetal Muscle Leg	muscle
13	chr17:38170000-38175200	Weak transcription	Brain Angular Gyrus	brain
14	chr17:38170000-38175600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr17:38170000-38176000	Enhancers	Ovary	ovary
16	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr17:38170200-38174400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr17:38170200-38174600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:38170200-38175400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:38170200-38175600	Weak transcription	Brain Substantia Nigra	brain
21	chr17:38170200-38175800	Weak transcription	Primary B cells from cord blood	blood
22	chr17:38170400-38174200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr17:38170400-38174200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr17:38170400-38174200	Enhancers	Stomach Smooth Muscle	stomach
25	chr17:38170400-38174600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:38170400-38175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr17:38170400-38175200	Weak transcription	Fetal Brain Male	brain
28	chr17:38170400-38175200	Weak transcription	Dnd41	blood
29	chr17:38170400-38177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr17:38171000-38174000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr17:38171000-38174000	Weak transcription	Left Ventricle	heart
33	chr17:38171000-38174200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:38171000-38174200	Weak transcription	NHDF-Ad	bronchial
35	chr17:38171000-38174400	Weak transcription	Esophagus	oesophagus
36	chr17:38171000-38174600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr17:38171000-38175200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr17:38171200-38175600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:38171400-38174200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr17:38171400-38174200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:38171400-38174400	Weak transcription	NH-A	brain
42	chr17:38171400-38174600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
44	chr17:38171600-38174000	Weak transcription	K562	blood
45	chr17:38171600-38174200	Weak transcription	A549	lung
46	chr17:38171600-38175200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr17:38171600-38176800	Weak transcription	Hela-S3	cervix
48	chr17:38171800-38174000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr17:38171800-38174200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr17:38171800-38174400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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