Variant report

Variant	rs928938
Chromosome Location	chr19:35818685-35818686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:132)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:132 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:35818664-35818890	GM12878	blood:	n/a	n/a
2	SMC3	chr19:35818586-35818918	HepG2	liver:	n/a	n/a
3	CTCF	chr19:35818640-35818790	HA-sp	spinal cord:	n/a	n/a
4	CTCF	chr19:35818616-35818925	MCF-7	breast:	n/a	n/a
5	CTCF	chr19:35818680-35818970	A549	lung:	n/a	n/a
6	BHLHE40	chr19:35818640-35818858	K562	blood:	n/a	n/a
7	CTCF	chr19:35818680-35818830	BE2_C	brain:	n/a	n/a
8	ZNF384	chr19:35818650-35818850	K562	blood:	n/a	n/a
9	RAD21	chr19:35818546-35819014	MCF-7	breast:	n/a	n/a
10	ATF1	chr19:35818599-35818885	K562	blood:	n/a	n/a
11	CTCF	chr19:35818660-35818810	HEEpiC	esophagus:	n/a	n/a
12	CTCF	chr19:35818671-35818907	HepG2	liver:	n/a	n/a
13	CUX1	chr19:35818630-35818808	K562	blood:	n/a	n/a
14	MAZ	chr19:35818586-35818922	K562	blood:	n/a	n/a
15	RAD21	chr19:35818518-35818921	HepG2	liver:	n/a	n/a
16	CTCF	chr19:35818680-35818830	GM12865	blood:	n/a	n/a
17	CTCF	chr19:35818640-35818790	AoAF	blood vessel:	n/a	n/a
18	CTCF	chr19:35818640-35818790	SAEC	small airway:	n/a	n/a
19	CTCF	chr19:35818655-35818863	GM10248	blood:	n/a	n/a
20	CTCF	chr19:35818680-35818830	AoAF	blood vessel:	n/a	n/a
21	CTCF	chr19:35818660-35818810	HCPEpiC	choroid plexus:	n/a	n/a
22	CTCF	chr19:35818680-35818830	GM12875	blood:	n/a	n/a
23	RAD21	chr19:35818530-35818940	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr19:35818660-35818810	AG04450	lung:	n/a	n/a
25	CTCF	chr19:35818680-35818830	HMF	breast:	n/a	n/a
26	CTCF	chr19:35818500-35818750	GM12870	blood:	n/a	n/a
27	CTCF	chr19:35818580-35818730	HMEC	breast:	n/a	n/a
28	CTCF	chr19:35818458-35819094	K562	blood:	n/a	n/a
29	JUND	chr19:35818590-35818916	K562	blood:	n/a	n/a
30	CEBPB	chr19:35818488-35818784	K562	blood:	n/a	n/a
31	CTCF	chr19:35818660-35818810	SAEC	small airway:	n/a	n/a
32	CTCF	chr19:35818650-35818860	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr19:35818560-35818710	AG04450	lung:	n/a	n/a
34	CTCF	chr19:35818620-35818770	GM12878	blood:	n/a	n/a
35	RAD21	chr19:35818617-35818874	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr19:35818629-35818937	A549	lung:	n/a	n/a
37	SMC3	chr19:35818623-35818900	K562	blood:	n/a	n/a
38	CTCF	chr19:35818640-35818790	HFF-Myc	foreskin:	n/a	n/a
39	CTCF	chr19:35818639-35818915	GM19239	blood:	n/a	n/a
40	E2F6	chr19:35818671-35818839	K562	blood:	n/a	n/a
41	CTCF	chr19:35818541-35818874	HepG2	liver:	n/a	n/a
42	CTCF	chr19:35818670-35818882	GM12891	blood:	n/a	n/a
43	CTCF	chr19:35818680-35818830	GM12866	blood:	n/a	n/a
44	CTCF	chr19:35818680-35818830	GM12874	blood:	n/a	n/a
45	CTCF	chr19:35818662-35818889	Gliobla	brain:	n/a	n/a
46	CTCF	chr19:35818680-35818830	HCT-116	colon:	n/a	n/a
47	CTCF	chr19:35818680-35818830	HL-60	blood:	n/a	n/a
48	CTCF	chr19:35818677-35818849	GM20000	blood:	n/a	n/a
49	MAFK	chr19:35818670-35818790	K562	blood:	n/a	n/a
50	CTCF	chr19:35818660-35818810	NB4	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35812803..35814917-chr19:35816658..35818799,2	K562	blood:
2	chr19:35814978..35818843-chr19:35819737..35823316,4	K562	blood:
3	chr19:35758155..35760598-chr19:35818136..35820258,3	MCF-7	breast:
4	chr19:35759820..35760630-chr19:35818301..35819272,2	MCF-7	breast:
5	chr19:35757401..35760609-chr19:35817502..35820242,3	MCF-7	breast:

No data

Variant related genes	Relation type
CD22	TF binding region
ENSG00000269553	TF binding region
ENSG00000105698	Chromatin interaction
ENSG00000269553	Chromatin interaction
ENSG00000012124	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10153506	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11669734	0.88[CEU][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7251526	0.83[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap]
rs756796	0.94[CEU][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS 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	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
8	esv1828194	chr19:35812566-35865695	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs928938	CD22	cis	Thyroid	GTEx
rs928938	SIRT2	cis	cerebellum	SCAN
rs928938	GSK3A	cis	parietal	SCAN
rs928938	U62631.5	cis	Thyroid	GTEx
rs928938	MAG	cis	Thyroid	GTEx
rs928938	MAG	cis	lung	GTEx
rs928938	KCNN4	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35810400-35835200	Weak transcription	Fetal Lung	lung
2	chr19:35811600-35832200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:35812000-35819600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:35812000-35820000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:35812200-35819400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:35813400-35819800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr19:35814600-35819600	Enhancers	Primary B cells from cord blood	blood
8	chr19:35815400-35819600	Enhancers	Primary B cells from peripheral blood	blood
9	chr19:35815400-35819800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr19:35815600-35819600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:35816800-35819600	Weak transcription	GM12878-XiMat	blood
12	chr19:35817600-35844000	Weak transcription	Brain Angular Gyrus	brain
13	chr19:35817800-35818800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr19:35818000-35819600	Weak transcription	Ovary	ovary
15	chr19:35818000-35820000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:35818000-35820400	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:35818400-35818800	Enhancers	K562	blood
18	chr19:35818400-35819600	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr19:35818400-35820600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr19:35818400-35821600	Strong transcription	Brain Substantia Nigra	brain
21	chr19:35818600-35818800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr19:35818600-35818800	Enhancers	Spleen	Spleen
23	chr19:35818600-35819600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links