Variant report

Variant	rs2227336
Chromosome Location	chr17:38174855-38174856
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38173011-38174885	K562	blood:	n/a	n/a
2	POLR2A	chr17:38174448-38174925	HL-60	blood:	n/a	n/a
3	ESR1	chr17:38174827-38175148	T-47D	breast:	n/a	chr17:38175047-38175064 chr17:38175047-38175062
4	ESR1	chr17:38174846-38175283	ECC-1	luminal epithelium:	n/a	chr17:38175047-38175064 chr17:38175047-38175062
5	JUND	chr17:38174736-38175081	H1-hESC	embryonic stem cell:	n/a	chr17:38174947-38174956
6	SIN3A	chr17:38174718-38175348	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUND	chr17:38174771-38174970	H1-hESC	embryonic stem cell:	n/a	chr17:38174947-38174956
8	POLR2A	chr17:38170916-38176213	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr17:38173937-38175874	MCF10A-Er-Src	breast:	n/a	chr17:38174947-38174956
10	POLR2A	chr17:38170766-38176716	U87	brain:	n/a	n/a
11	FOS	chr17:38174729-38175146	MCF10A-Er-Src	breast:	n/a	chr17:38174947-38174956
12	POLR2A	chr17:38170628-38176722	U87	brain:	n/a	n/a
13	POLR2A	chr17:38171303-38175657	MCF10A-Er-Src	breast:	n/a	n/a
14	ZNF143	chr17:38174650-38175025	H1-hESC	embryonic stem cell:	n/a	chr17:38174937-38174955
15	ESR1	chr17:38174754-38175311	ECC-1	luminal epithelium:	n/a	chr17:38175047-38175064 chr17:38175047-38175062
16	CHD2	chr17:38174812-38175058	H1-hESC	embryonic stem cell:	n/a	n/a
17	ATF2	chr17:38174724-38175211	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr17:38173854-38176132	HUVEC	blood vessel:	n/a	n/a
19	TBP	chr17:38174798-38175253	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr17:38174529-38175169	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr17:38173296-38175247	K562	blood:	n/a	n/a
22	POLR2A	chr17:38174089-38176121	HUVEC	blood vessel:	n/a	n/a
23	TAF1	chr17:38174814-38175179	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr17:38171205-38176070	U87	brain:	n/a	n/a
25	MYC	chr17:38174774-38174967	H1-hESC	embryonic stem cell:	n/a	chr17:38174944-38174954
26	POLR2A	chr17:38173976-38176162	HUVEC	blood vessel:	n/a	n/a
27	ESR1	chr17:38174789-38175335	ECC-1	luminal epithelium:	n/a	chr17:38175047-38175064 chr17:38175047-38175062
28	POLR2A	chr17:38174193-38174858	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38174242..38176838-chr17:38278779..38280861,2	MCF-7	breast:
2	chr17:38172520..38175725-chr17:38187607..38191443,4	MCF-7	breast:
3	chr17:38174715..38177590-chr17:38209751..38212777,3	K562	blood:
4	chr17:38169328..38171805-chr17:38172299..38175519,5	K562	blood:
5	chr17:38174842..38178903-chr17:38208625..38211251,3	K562	blood:
6	chr17:38172859..38176802-chr17:38178682..38181500,4	K562	blood:
7	chr17:38141745..38144493-chr17:38173834..38176591,2	MCF-7	breast:
8	chr17:38173047..38175621-chr17:38177692..38179979,3	MCF-7	breast:
9	chr17:38171100..38173173-chr17:38173231..38176436,3	K562	blood:
10	chr17:38143597..38146360-chr17:38172431..38175405,3	K562	blood:
11	chr17:38172636..38175341-chr17:38255721..38258482,3	MCF-7	breast:
12	chr17:38169328..38171032-chr17:38172943..38175519,2	K562	blood:

Variant related genes	Relation type
ENSG00000265799	TF binding region
ENSG00000265799	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000108342	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1042658	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045929	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078934	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11871747	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12600856	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12602172	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12941811	0.89[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	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227322	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213762	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826331	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3884477	0.86[ASN][1000 genomes]
rs3935280	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3936197	0.86[ASN][1000 genomes]
rs4794822	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4794823	0.91[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	0.87[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	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4795419	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4795420	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55771023	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55846942	0.87[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	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57968500	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59925331	0.92[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6503530	0.91[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	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs709591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208815	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7209755	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214085	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221894	0.89[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	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7502912	0.82[ASN][1000 genomes]
rs7503555	0.84[ASN][1000 genomes]
rs8065443	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]
rs8066846	0.84[ASN][1000 genomes]
rs8067817	0.85[ASN][1000 genomes]
rs8068260	0.81[ASN][1000 genomes]
rs8070454	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8072548	0.85[ASN][1000 genomes]
rs8078692	0.84[ASN][1000 genomes]
rs8078723	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8081692	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs868150	0.86[ASN][1000 genomes]
rs9303283	0.88[ASN][1000 genomes]
rs9303284	0.87[ASN][1000 genomes]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2227336	MED24	cis	Artery Aorta	GTEx
rs2227336	GSDMA	cis	Adipose Subcutaneous	GTEx
rs2227336	GSDMA	cis	Esophagus Muscularis	GTEx
rs2227336	MED24	cis	Thyroid	GTEx
rs2227336	MED24	cis	Artery Tibial	GTEx
rs2227336	GSDMA	cis	lung	GTEx
rs2227336	MED24	cis	Nerve Tibial	GTEx
rs2227336	GSDMA	cis	Artery Aorta	GTEx
rs2227336	GSDMA	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:38169600-38175000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr17:38169800-38175600	Enhancers	Fetal Lung	lung
6	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:38170000-38175200	Weak transcription	Brain Angular Gyrus	brain
8	chr17:38170000-38175600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr17:38170000-38176000	Enhancers	Ovary	ovary
10	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr17:38170200-38175400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:38170200-38175600	Weak transcription	Brain Substantia Nigra	brain
13	chr17:38170200-38175800	Weak transcription	Primary B cells from cord blood	blood
14	chr17:38170400-38175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:38170400-38175200	Weak transcription	Fetal Brain Male	brain
16	chr17:38170400-38175200	Weak transcription	Dnd41	blood
17	chr17:38170400-38177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr17:38171000-38175200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:38171200-38175600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
22	chr17:38171600-38175200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:38171600-38176800	Weak transcription	Hela-S3	cervix
24	chr17:38171800-38175200	Weak transcription	Fetal Thymus	thymus
25	chr17:38172000-38175000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:38172000-38175600	Weak transcription	GM12878-XiMat	blood
27	chr17:38172200-38176000	Enhancers	HUVEC	blood vessel
28	chr17:38172400-38175600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr17:38172400-38175800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr17:38172400-38178400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr17:38172800-38176800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:38173000-38176600	Genic enhancers	Fetal Stomach	stomach
33	chr17:38173000-38179600	Strong transcription	Fetal Intestine Small	intestine
34	chr17:38173000-38181400	Weak transcription	Fetal Kidney	kidney
35	chr17:38173200-38175000	Genic enhancers	HMEC	breast
36	chr17:38173200-38176800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr17:38173400-38175000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr17:38173600-38175400	Enhancers	Fetal Heart	heart
41	chr17:38173600-38176600	Enhancers	Psoas Muscle	Psoas
42	chr17:38173600-38180200	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr17:38173600-38180400	Genic enhancers	NHLF	lung
44	chr17:38173600-38182000	Strong transcription	Thymus	Thymus
45	chr17:38173800-38175000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr17:38173800-38175800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr17:38173800-38176000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr17:38173800-38176000	Enhancers	Right Atrium	heart
49	chr17:38173800-38176800	Enhancers	Stomach Mucosa	stomach
50	chr17:38173800-38179400	Strong transcription	Fetal Intestine Large	intestine

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