Variant report

Variant	rs28694624
Chromosome Location	chr19:23466814-23466815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:23466812-23467044	GM13977	blood:	n/a	n/a
2	RAD21	chr19:23466723-23467108	HepG2	liver:	n/a	n/a
3	CTCF	chr19:23466789-23467056	Gliobla	brain:	n/a	n/a
4	CTCF	chr19:23466805-23467040	MCF-7	breast:	n/a	n/a
5	CTCF	chr19:23466782-23467062	H1-hESC	embryonic stem cell:	n/a	n/a
6	ARID3A	chr19:23466709-23467067	HepG2	liver:	n/a	n/a
7	YY1	chr19:23466812-23467011	GM12878	blood:	n/a	n/a
8	CTCF	chr19:23466764-23467107	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr19:23466636-23467117	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr19:23466813-23467037	GM12892	blood:	n/a	n/a
11	CTCF	chr19:23466773-23467085	K562	blood:	n/a	n/a
12	CTCF	chr19:23466780-23466930	MCF-7	breast:	n/a	n/a
13	ZNF143	chr19:23466750-23467090	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr19:23466804-23467075	Kidney_OC	kidney:	n/a	n/a
15	RAD21	chr19:23466808-23467141	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr19:23466811-23467046	GM12878	blood:	n/a	n/a
17	CTCF	chr19:23466793-23467041	Fibrobl	skin:	n/a	n/a
18	SMC3	chr19:23466528-23467232	SK-N-SH	brain:	n/a	n/a
19	RAD21	chr19:23466703-23467081	HepG2	liver:	n/a	n/a
20	CTCF	chr19:23466716-23467109	GM12878	blood:	n/a	n/a
21	ZNF143	chr19:23466790-23466990	K562	blood:	n/a	n/a
22	CTCF	chr19:23466760-23467121	IMR90	lung:	n/a	n/a
23	CTCF	chr19:23466756-23467112	HepG2	liver:	n/a	n/a
24	CTCF	chr19:23466802-23466989	HepG2	liver:	n/a	n/a
25	SMC3	chr19:23466802-23467094	GM12878	blood:	n/a	n/a
26	RAD21	chr19:23466760-23467099	IMR90	lung:	n/a	n/a
27	PAX5	chr19:23466805-23467030	GM12878	blood:	n/a	n/a
28	RAD21	chr19:23466767-23467007	SK-N-SH_RA	brain:	n/a	n/a
29	CTCF	chr19:23466719-23467169	A549	lung:	n/a	n/a
30	CTCF	chr19:23466811-23467060	GM19238	blood:	n/a	n/a
31	CTCF	chr19:23466778-23467045	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr19:23466802-23467053	ProgFib	skin:	n/a	n/a
33	CTCF	chr19:23466800-23466950	GM12868	blood:	n/a	n/a
34	RAD21	chr19:23466760-23467094	HepG2	liver:	n/a	n/a
35	CTCF	chr19:23466597-23467215	SK-N-SH	brain:	n/a	n/a
36	JUND	chr19:23466814-23467052	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr19:23466800-23467043	GM12891	blood:	n/a	n/a
38	CTCF	chr19:23466803-23467014	SK-N-SH_RA	brain:	n/a	n/a
39	CTCF	chr19:23466767-23467008	K562	blood:	n/a	n/a
40	RAD21	chr19:23466523-23467147	SK-N-SH	brain:	n/a	n/a
41	RAD21	chr19:23466708-23467107	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr19:23466781-23467117	SK-N-SH_RA	brain:	n/a	n/a
43	MXI1	chr19:23466705-23467189	SK-N-SH	brain:	n/a	n/a
44	ZNF143	chr19:23466787-23467038	GM12878	blood:	n/a	n/a
45	RAD21	chr19:23466754-23467035	GM12878	blood:	n/a	n/a
46	CTCF	chr19:23466795-23467094	Spleen_OC	spleen:	n/a	n/a
47	CTCF	chr19:23466797-23467033	SK-N-SH_RA	brain:	n/a	n/a
48	SMC3	chr19:23466720-23467123	HepG2	liver:	n/a	n/a
49	MAX	chr19:23466807-23467108	NB4	blood:	n/a	n/a
50	RAD21	chr19:23466776-23467090	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:23456110..23458063-chr19:23465875..23467770,2	MCF-7	breast:

No data

Variant related genes	Relation type
VN1R90P	TF binding region
ENSG00000213971	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1650857	0.88[EUR][1000 genomes]
rs1658216	0.82[EUR][1000 genomes]
rs28609324	0.83[AFR][1000 genomes]
rs370642	0.88[EUR][1000 genomes]
rs374765	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs386995	0.88[EUR][1000 genomes]
rs388346	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs392578	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs409689	0.81[EUR][1000 genomes]
rs418980	0.85[EUR][1000 genomes]
rs423289	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs435002	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs437313	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs451707	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs454059	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs454641	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs493697	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs572210	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34470	chr19:22922549-23659458	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
2	esv34907	chr19:22922549-23683097	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
3	nsv9686	chr19:22989454-23653750	Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
4	nsv817826	chr19:23000745-23620632	Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	esv3693269	chr19:23000745-23652839	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
6	esv2758491	chr19:23071299-23940467	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1065157	chr19:23091826-23812323	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
8	nsv543959	chr19:23091826-23812323	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	esv3424935	chr19:23111817-23495542	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
10	esv3429878	chr19:23246650-23590744	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	esv3410568	chr19:23246670-23590714	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	esv3433243	chr19:23249108-23585814	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
13	esv3387823	chr19:23265885-23590028	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
14	esv3321838	chr19:23303462-23482478	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv833789	chr19:23329463-23487797	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	esv3440847	chr19:23361380-23481908	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	esv3446056	chr19:23361400-23481878	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv579034	chr19:23387788-23610784	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
19	nsv833790	chr19:23405972-23557520	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
20	esv3332495	chr19:23451842-23598069	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
21	esv3319024	chr19:23456003-23598068	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
22	esv3319025	chr19:23456003-23598068	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
23	esv3317831	chr19:23463612-23468710	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	esv3524802	chr19:23464012-23467910	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	esv3317830	chr19:23464137-23467985	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	esv1819260	chr19:23464386-23471341	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	esv3317825	chr19:23464732-23467209	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	esv3524801	chr19:23464787-23467810	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
29	esv3317824	chr19:23465007-23466847	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	esv3524797	chr19:23465032-23466930	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
31	esv3447830	chr19:23465035-23610690	Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
32	esv3524798	chr19:23465045-23466869	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
33	esv3317828	chr19:23465063-23466887	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
34	esv3524799	chr19:23465063-23466894	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
35	esv3524800	chr19:23465072-23466877	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
36	esv3524803	chr19:23465072-23466894	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
37	esv3317826	chr19:23465074-23466872	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
38	nsv138139	chr19:23465193-23466837	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23457600-23470400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr19:23464200-23467000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr19:23464400-23467000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr19:23466000-23467000	Enhancers	HepG2	liver
5	chr19:23466400-23470600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:23466600-23467000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:23466600-23467200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr19:23466800-23467000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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