Variant report

Variant	rs2075657
Chromosome Location	chr17:18061528-18061529
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	TBP	chr17:18061237-18061722	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr17:18061305-18061800	GM12878	blood:	n/a	chr17:18061560-18061572 chr17:18061562-18061571 chr17:18061626-18061635 chr17:18061562-18061571 chr17:18061561-18061570 chr17:18061324-18061334 chr17:18061560-18061571 chr17:18061561-18061571 chr17:18061324-18061334 chr17:18061560-18061572
3	NFIC	chr17:18061230-18061974	ECC-1	luminal epithelium:	n/a	n/a
4	TBL1XR1	chr17:18061388-18061606	K562	blood:	n/a	n/a
5	CHD2	chr17:18061272-18061625	H1-hESC	embryonic stem cell:	n/a	n/a
6	FOS	chr17:18061456-18061700	MCF10A-Er-Src	breast:	n/a	n/a
7	SP4	chr17:18061247-18061778	H1-hESC	embryonic stem cell:	n/a	chr17:18061558-18061574 chr17:18061560-18061571 chr17:18061321-18061337 chr17:18061607-18061623
8	WRNIP1	chr17:18061481-18061860	GM12878	blood:	n/a	n/a
9	ZEB1	chr17:18061070-18061851	GM12878	blood:	n/a	chr17:18061378-18061385 chr17:18061531-18061538
10	POLR2A	chr17:18061251-18061858	HCT-116	colon:	n/a	n/a
11	HMGN3	chr17:18060974-18062050	K562	blood:	n/a	n/a
12	GTF2F1	chr17:18061325-18061623	H1-hESC	embryonic stem cell:	n/a	n/a
13	TBP	chr17:18061369-18061928	K562	blood:	n/a	n/a
14	EP300	chr17:18061337-18061950	GM12878	blood:	n/a	chr17:18061487-18061496 chr17:18061374-18061390
15	GTF2F1	chr17:18061372-18061535	K562	blood:	n/a	n/a
16	MTA3	chr17:18061206-18061661	GM12878	blood:	n/a	n/a
17	POLR2A	chr17:18061441-18061877	GM12878	blood:	n/a	n/a
18	ELF1	chr17:18061420-18061759	A549	lung:	n/a	chr17:18061586-18061599
19	RFX5	chr17:18061441-18061759	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:18061366-18061927	GM12878	blood:	n/a	n/a
21	GABPA	chr17:18061373-18061795	K562	blood:	n/a	n/a
22	CREB1	chr17:18061268-18061861	H1-hESC	embryonic stem cell:	n/a	chr17:18061575-18061588
23	SIN3A	chr17:18061483-18061770	GM12878	blood:	n/a	n/a
24	POLR2A	chr17:18061338-18061904	GM15510	blood:	n/a	n/a
25	POLR2A	chr17:18061473-18061833	MCF10A-Er-Src	breast:	n/a	n/a
26	ELF1	chr17:18061399-18061877	MCF-7	breast:	n/a	chr17:18061586-18061599
27	TAF1	chr17:18061234-18061536	H1-hESC	embryonic stem cell:	n/a	n/a
28	ELK1	chr17:18061408-18061651	K562	blood:	n/a	n/a
29	EGR1	chr17:18061279-18061821	H1-hESC	embryonic stem cell:	n/a	chr17:18061717-18061730 chr17:18061659-18061670 chr17:18061533-18061546 chr17:18061654-18061676 chr17:18061658-18061671 chr17:18061658-18061671 chr17:18061532-18061547 chr17:18061660-18061670 chr17:18061534-18061545 chr17:18061533-18061546 chr17:18061659-18061670 chr17:18061712-18061727 chr17:18061660-18061670 chr17:18061658-18061671 chr17:18061535-18061545 chr17:18061661-18061670 chr17:18061533-18061546 chr17:18061658-18061672 chr17:18061717-18061730 chr17:18061657-18061672 chr17:18061533-18061547 chr17:18061716-18061731 chr17:18061658-18061671 chr17:18061529-18061551
30	EGR1	chr17:18061287-18061956	MCF-7	breast:	n/a	chr17:18061717-18061730 chr17:18061659-18061670 chr17:18061533-18061546 chr17:18061654-18061676 chr17:18061658-18061671 chr17:18061658-18061671 chr17:18061532-18061547 chr17:18061660-18061670 chr17:18061534-18061545 chr17:18061533-18061546 chr17:18061659-18061670 chr17:18061712-18061727 chr17:18061660-18061670 chr17:18061658-18061671 chr17:18061535-18061545 chr17:18061661-18061670 chr17:18061533-18061546 chr17:18061658-18061672 chr17:18061717-18061730 chr17:18061657-18061672 chr17:18061533-18061547 chr17:18061716-18061731 chr17:18061658-18061671 chr17:18061529-18061551
31	USF2	chr17:18061438-18061893	GM12878	blood:	n/a	n/a
32	CUX1	chr17:18061336-18061536	K562	blood:	n/a	n/a
33	EGR1	chr17:18061401-18061798	GM12878	blood:	n/a	chr17:18061717-18061730 chr17:18061659-18061670 chr17:18061533-18061546 chr17:18061654-18061676 chr17:18061658-18061671 chr17:18061658-18061671 chr17:18061532-18061547 chr17:18061660-18061670 chr17:18061534-18061545 chr17:18061533-18061546 chr17:18061659-18061670 chr17:18061712-18061727 chr17:18061660-18061670 chr17:18061658-18061671 chr17:18061535-18061545 chr17:18061661-18061670 chr17:18061533-18061546 chr17:18061658-18061672 chr17:18061717-18061730 chr17:18061657-18061672 chr17:18061533-18061547 chr17:18061716-18061731 chr17:18061658-18061671 chr17:18061529-18061551
34	MAX	chr17:18061316-18062008	GM12878	blood:	n/a	chr17:18061660-18061669
35	PAX5	chr17:18061459-18061724	GM12878	blood:	n/a	n/a
36	POLR2A	chr17:18061289-18061708	H1-hESC	embryonic stem cell:	n/a	n/a
37	CREB1	chr17:18061308-18061847	K562	blood:	n/a	chr17:18061575-18061588
38	FOS	chr17:18061442-18061642	MCF10A-Er-Src	breast:	n/a	n/a
39	MAZ	chr17:18061299-18062036	GM12878	blood:	n/a	chr17:18061660-18061669
40	RCOR1	chr17:18061333-18061816	K562	blood:	n/a	n/a
41	EGR1	chr17:18061263-18061998	ECC-1	luminal epithelium:	n/a	chr17:18061717-18061730 chr17:18061659-18061670 chr17:18061533-18061546 chr17:18061654-18061676 chr17:18061658-18061671 chr17:18061658-18061671 chr17:18061532-18061547 chr17:18061660-18061670 chr17:18061534-18061545 chr17:18061533-18061546 chr17:18061659-18061670 chr17:18061712-18061727 chr17:18061660-18061670 chr17:18061658-18061671 chr17:18061535-18061545 chr17:18061661-18061670 chr17:18061533-18061546 chr17:18061658-18061672 chr17:18061717-18061730 chr17:18061657-18061672 chr17:18061533-18061547 chr17:18061716-18061731 chr17:18061658-18061671 chr17:18061529-18061551
42	CREB1	chr17:18061456-18061770	A549	lung:	n/a	chr17:18061575-18061588
43	POLR2A	chr17:18061337-18061842	GM12878	blood:	n/a	n/a
44	USF1	chr17:18061307-18061637	H1-hESC	embryonic stem cell:	n/a	n/a
45	RFX5	chr17:18061471-18061597	HepG2	liver:	n/a	n/a
46	CREB1	chr17:18061327-18061803	ECC-1	luminal epithelium:	n/a	chr17:18061575-18061588
47	EGR1	chr17:18061258-18062023	MCF-7	breast:	n/a	chr17:18061717-18061730 chr17:18061659-18061670 chr17:18061533-18061546 chr17:18061654-18061676 chr17:18061658-18061671 chr17:18061658-18061671 chr17:18061532-18061547 chr17:18061660-18061670 chr17:18061534-18061545 chr17:18061533-18061546 chr17:18061659-18061670 chr17:18061712-18061727 chr17:18061660-18061670 chr17:18061658-18061671 chr17:18061535-18061545 chr17:18061661-18061670 chr17:18061533-18061546 chr17:18061658-18061672 chr17:18061717-18061730 chr17:18061657-18061672 chr17:18061533-18061547 chr17:18061716-18061731 chr17:18061658-18061671 chr17:18061529-18061551
48	SP1	chr17:18061316-18061775	K562	blood:	n/a	chr17:18061560-18061572 chr17:18061562-18061571 chr17:18061626-18061635 chr17:18061562-18061571 chr17:18061561-18061570 chr17:18061324-18061334 chr17:18061560-18061571 chr17:18061561-18061571 chr17:18061324-18061334 chr17:18061560-18061572
49	CHD2	chr17:18061431-18062017	GM12878	blood:	n/a	n/a
50	CEBPB	chr17:18061316-18061711	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18059406..18063498-chr17:18086302..18089651,4	K562	blood:
2	chr17:18057503..18062681-chr17:18084968..18089396,8	MCF-7	breast:
3	chr17:18059834..18062065-chr17:18216789..18219409,3	MCF-7	breast:
4	chr17:18057350..18061680-chr17:18083813..18088656,8	K562	blood:
5	chr17:18057330..18058891-chr17:18059852..18061611,2	MCF-7	breast:
6	chr17:18055989..18058847-chr17:18059352..18061809,2	K562	blood:

Variant related genes	Relation type
MYO15A	TF binding region
ENSG00000091542	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000091536	Chromatin interaction
ENSG00000176994	Chromatin interaction
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12051649	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075658	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2245430	0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs2473656	0.95[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605133	0.84[EUR][1000 genomes]
rs2856289	0.84[EUR][1000 genomes]
rs4925144	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59588957	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712271	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs712274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72831919	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854773	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854774	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854777	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs854778	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs854780	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs854783	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs854796	0.99[ASN][1000 genomes]
rs854800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854803	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9899249	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9903403	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9903591	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9913262	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription 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	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2075657	LGALS9C	cis	Whole Blood	GTEx
rs2075657	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs2075657	SHMT1	cis	Whole Blood	GTEx
rs2075657	USP32P2	cis	Thyroid	GTEx
rs2075657	FAM106A	cis	Thyroid	GTEx
rs2075657	SHMT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18057600-18061600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:18057600-18061600	Weak transcription	Liver	Liver
3	chr17:18057600-18061600	Weak transcription	Brain Anterior Caudate	brain
4	chr17:18057600-18061600	Weak transcription	Psoas Muscle	Psoas
5	chr17:18057600-18061600	Weak transcription	NH-A	brain
6	chr17:18057600-18061800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:18057600-18061800	Weak transcription	NHDF-Ad	bronchial
8	chr17:18057600-18063000	Weak transcription	HSMMtube	muscle
9	chr17:18057800-18061600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr17:18057800-18061800	Weak transcription	Stomach Mucosa	stomach
11	chr17:18058200-18061600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:18058200-18061600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr17:18058800-18061800	Weak transcription	Fetal Brain Male	brain
14	chr17:18059200-18061600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr17:18059200-18062600	Enhancers	Spleen	Spleen
16	chr17:18059400-18061600	Enhancers	GM12878-XiMat	blood
17	chr17:18059800-18061600	Enhancers	K562	blood
18	chr17:18060200-18061800	Weak transcription	NHLF	lung
19	chr17:18060400-18061600	Enhancers	Fetal Muscle Trunk	muscle
20	chr17:18060800-18061600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr17:18060800-18061600	Enhancers	Primary B cells from cord blood	blood
22	chr17:18060800-18061600	Enhancers	Placenta	Placenta
23	chr17:18060800-18061600	Enhancers	HMEC	breast
24	chr17:18060800-18062600	Weak transcription	A549	lung
25	chr17:18061000-18061600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:18061000-18061600	Enhancers	Lung	lung
27	chr17:18061000-18061800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:18061000-18062200	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr17:18061000-18062400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr17:18061200-18061600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:18061200-18061600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr17:18061200-18061600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr17:18061200-18061600	Enhancers	Esophagus	oesophagus
34	chr17:18061200-18061600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr17:18061200-18061800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:18061200-18062000	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr17:18061200-18062000	Active TSS	H1 Cell Line	embryonic stem cell
38	chr17:18061200-18062000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr17:18061200-18062000	Active TSS	Fetal Kidney	kidney
40	chr17:18061200-18062200	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr17:18061200-18062200	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr17:18061200-18062200	Flanking Active TSS	Fetal Stomach	stomach
43	chr17:18061200-18062200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr17:18061200-18062200	Enhancers	Small Intestine	intestine
45	chr17:18061200-18062400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:18061200-18062400	Enhancers	Fetal Heart	heart
47	chr17:18061200-18062600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:18061400-18061600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr17:18061400-18061600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr17:18061400-18061600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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