Variant report

Variant	rs7213472
Chromosome Location	chr17:18267209-18267210
allele	C/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	chr17:18266476-18267243	HUVEC	blood vessel:	n/a	n/a
2	MAX	chr17:18265999-18267224	Hela-S3	cervix:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
3	POLR2A	chr17:18266427-18267231	GM12892	blood:	n/a	n/a
4	HCFC1	chr17:18265849-18267418	Hela-S3	cervix:	n/a	n/a
5	SIN3A	chr17:18265943-18267245	H1-hESC	embryonic stem cell:	n/a	chr17:18266500-18266511 chr17:18266772-18266781 chr17:18266770-18266779 chr17:18266753-18266764
6	STAT3	chr17:18267048-18267244	MCF10A-Er-Src	breast:	n/a	chr17:18267070-18267084 chr17:18267073-18267082 chr17:18267072-18267081
7	POLR2A	chr17:18266415-18267264	ECC-1	luminal epithelium:	n/a	n/a
8	MAZ	chr17:18266647-18267441	GM12878	blood:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
9	PML	chr17:18266426-18267221	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:18266505-18267247	GM12891	blood:	n/a	n/a
11	POLR2A	chr17:18266369-18267222	PFSK-1	brain:	n/a	n/a
12	USF1	chr17:18266304-18267225	HCT-116	colon:	n/a	chr17:18266498-18266514 chr17:18266949-18266965 chr17:18266562-18266578
13	CUX1	chr17:18267006-18267222	K562	blood:	n/a	n/a
14	USF2	chr17:18266212-18267212	Hela-S3	cervix:	n/a	chr17:18266770-18266781 chr17:18266498-18266514 chr17:18266949-18266965 chr17:18266562-18266578
15	POLR2A	chr17:18266463-18267213	HCT-116	colon:	n/a	n/a
16	TCF12	chr17:18265811-18267244	A549	lung:	n/a	n/a
17	MTA3	chr17:18266846-18267216	GM12878	blood:	n/a	n/a
18	MYC	chr17:18266463-18267427	K562	blood:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
19	TBP	chr17:18266645-18267238	Hela-S3	cervix:	n/a	n/a
20	MAZ	chr17:18266084-18267221	Hela-S3	cervix:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
21	TAF7	chr17:18266550-18267230	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr17:18265989-18267229	HepG2	liver:	n/a	n/a
23	POLR2A	chr17:18266464-18267250	HEK293	kidney:	n/a	n/a
24	BRCA1	chr17:18266021-18267215	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr17:18266115-18267261	Raji	blood:	n/a	n/a
26	POLR2A	chr17:18266602-18267233	HCT-116	colon:	n/a	n/a
27	JUND	chr17:18266542-18267218	A549	lung:	n/a	n/a
28	CHD2	chr17:18266174-18267227	H1-hESC	embryonic stem cell:	n/a	chr17:18266975-18266985
29	GATA1	chr17:18266084-18267223	PBDE	blood:	n/a	n/a
30	CREB1	chr17:18266394-18267262	HepG2	liver:	n/a	n/a
31	PML	chr17:18266450-18267221	MCF-7	breast:	n/a	n/a
32	MAX	chr17:18265865-18267211	HepG2	liver:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
33	SP1	chr17:18266403-18267220	A549	lung:	n/a	chr17:18266866-18266875 chr17:18266975-18266984 chr17:18266881-18266902 chr17:18266866-18266876 chr17:18266865-18266877 chr17:18266865-18266876 chr17:18266867-18266876 chr17:18266865-18266877 chr17:18266866-18266875 chr17:18266866-18266876 chr17:18267013-18267022
34	TAF1	chr17:18266416-18267248	A549	lung:	n/a	n/a
35	POLR2A	chr17:18266492-18267236	K562	blood:	n/a	n/a
36	NRF1	chr17:18265905-18267251	SK-N-SH	brain:	n/a	chr17:18266998-18267009 chr17:18266867-18266876 chr17:18266954-18266963
37	TCF12	chr17:18266625-18267249	A549	lung:	n/a	n/a
38	POLR2A	chr17:18266485-18267246	NB4	blood:	n/a	n/a
39	SP1	chr17:18266562-18267289	A549	lung:	n/a	chr17:18266866-18266875 chr17:18266975-18266984 chr17:18266881-18266902 chr17:18266866-18266876 chr17:18266865-18266877 chr17:18266865-18266876 chr17:18266867-18266876 chr17:18266865-18266877 chr17:18266866-18266875 chr17:18266866-18266876 chr17:18267013-18267022
40	POLR2A	chr17:18266487-18267238	GM19099	blood:	n/a	n/a
41	TAF1	chr17:18266380-18267272	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr17:18266436-18267222	GM12892	blood:	n/a	n/a
43	POLR2A	chr17:18266509-18267226	HepG2	liver:	n/a	n/a
44	TAF1	chr17:18266438-18267277	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr17:18266385-18267238	GM18505	blood:	n/a	n/a
46	POLR2A	chr17:18266458-18267225	HCT-116	colon:	n/a	n/a
47	POLR2A	chr17:18266397-18267223	U87	brain:	n/a	n/a
48	POLR2A	chr17:18266484-18267226	GM18526	blood:	n/a	n/a
49	POLR2A	chr17:18266003-18267243	Hela-S3	cervix:	n/a	n/a
50	CEBPB	chr17:18265923-18267214	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18267096..18271121-chr17:18271318..18274892,4	K562	blood:

Variant related genes	Relation type
SHMT1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs28694704	1.00[EUR][1000 genomes]
rs56109231	1.00[EUR][1000 genomes]
rs56180580	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56735648	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56793258	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58115308	1.00[EUR][1000 genomes]
rs58499955	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59738176	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59867698	1.00[EUR][1000 genomes]
rs60320587	1.00[EUR][1000 genomes]
rs60510653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60699593	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60708953	1.00[EUR][1000 genomes]
rs60814048	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61361031	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61576260	1.00[EUR][1000 genomes]
rs7207131	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7207489	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7213789	1.00[EUR][1000 genomes]
rs7219191	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7226015	1.00[EUR][1000 genomes]
rs73288279	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288297	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288302	1.00[EUR][1000 genomes]
rs73289913	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8064901	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068530	1.00[EUR][1000 genomes]
rs8069012	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8071028	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8071911	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8074322	1.00[EUR][1000 genomes]
rs8080816	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9910599	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
4	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
5	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases
8	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
12	nsv827913	chr17:18253785-18572122	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1065708	chr17:18259174-18913343	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18265200-18267400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:18265400-18267400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr17:18265800-18267400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:18265800-18267400	Active TSS	Hela-S3	cervix
5	chr17:18265800-18267600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr17:18266000-18267400	Active TSS	K562	blood
7	chr17:18266200-18267400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr17:18266200-18267600	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr17:18266400-18267400	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr17:18266400-18267400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:18266600-18267400	Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr17:18266600-18267400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr17:18266600-18267400	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr17:18266600-18267400	Active TSS	Stomach Smooth Muscle	stomach
15	chr17:18267000-18267400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr17:18267000-18267400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr17:18267000-18267400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr17:18267000-18267400	Flanking Active TSS	Dnd41	blood
19	chr17:18267200-18267400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr17:18267200-18267400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr17:18267200-18267400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr17:18267200-18267400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:18267200-18267400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:18267200-18267400	Enhancers	Brain Germinal Matrix	brain
25	chr17:18267200-18267400	Enhancers	Fetal Intestine Large	intestine
26	chr17:18267200-18267400	Active TSS	Thymus	Thymus
27	chr17:18267200-18267600	Enhancers	Primary B cells from cord blood	blood
28	chr17:18267200-18267600	Enhancers	Primary B cells from peripheral blood	blood
29	chr17:18267200-18267600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr17:18267200-18267600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr17:18267200-18267600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:18267200-18267600	Enhancers	Duodenum Mucosa	Duodenum
33	chr17:18267200-18267600	Enhancers	Fetal Lung	lung
34	chr17:18267200-18267600	Enhancers	Fetal Muscle Trunk	muscle
35	chr17:18267200-18267600	Enhancers	GM12878-XiMat	blood
36	chr17:18267200-18267600	Enhancers	HMEC	breast
37	chr17:18267200-18268000	Enhancers	Liver	Liver
38	chr17:18267200-18268000	Enhancers	Fetal Thymus	thymus
39	chr17:18267200-18271800	Weak transcription	Placenta	Placenta
40	chr17:18267200-18274600	Weak transcription	NHEK	skin
41	chr17:18267200-18288200	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links