Variant report

Variant	rs469189
Chromosome Location	chr22:29949509-29949510
allele	A/G
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	HEY1	chr22:29949453-29950076	K562	blood:	n/a	n/a
2	POLR2A	chr22:29949476-29950021	GM12891	blood:	n/a	n/a
3	TAF1	chr22:29949168-29950049	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr22:29949337-29950319	GM18505	blood:	n/a	n/a
5	RUNX3	chr22:29949253-29950044	GM12878	blood:	n/a	n/a
6	GABPA	chr22:29949300-29949976	K562	blood:	n/a	n/a
7	TAF1	chr22:29949478-29949995	SK-N-SH	brain:	n/a	n/a
8	ETS1	chr22:29949456-29950003	K562	blood:	n/a	chr22:29949738-29949747 chr22:29949764-29949774 chr22:29949738-29949747 chr22:29949763-29949772 chr22:29949738-29949747 chr22:29949763-29949772 chr22:29949783-29949794 chr22:29949763-29949772 chr22:29949737-29949746 chr22:29949763-29949772 chr22:29949739-29949749 chr22:29949738-29949747 chr22:29949735-29949748 chr22:29949738-29949747 chr22:29949763-29949772 chr22:29949763-29949772 chr22:29949738-29949747 chr22:29949736-29949745 chr22:29949734-29949750 chr22:29949760-29949773 chr22:29949738-29949747
9	TCF12	chr22:29949254-29950095	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr22:29949314-29950424	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr22:29949083-29950345	H1-neurons	neurons:	n/a	chr22:29949588-29949602 chr22:29949405-29949418
12	MXI1	chr22:29949211-29950461	IMR90	lung:	n/a	n/a
13	ELK1	chr22:29949505-29950001	Hela-S3	cervix:	n/a	chr22:29949738-29949747 chr22:29949763-29949772 chr22:29949738-29949747 chr22:29949763-29949772
14	MYC	chr22:29949258-29950140	MCF10A-Er-Src	breast:	n/a	chr22:29949844-29949854
15	TAF7	chr22:29949428-29949971	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr22:29949393-29950319	PANC-1	pancreas:	n/a	n/a
17	GABPA	chr22:29949243-29950291	HL-60	blood:	n/a	n/a
18	ZMIZ1	chr22:29949439-29950127	K562	blood:	n/a	n/a
19	RFX5	chr22:29949376-29950149	HepG2	liver:	n/a	n/a
20	POLR2A	chr22:29949366-29950092	GM19099	blood:	n/a	n/a
21	POLR2A	chr22:29949303-29950060	K562	blood:	n/a	n/a
22	TAF1	chr22:29948828-29950350	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr22:29949400-29950102	SK-N-MC	brain:	n/a	n/a
24	BCL3	chr22:29949498-29950354	A549	lung:	n/a	chr22:29949738-29949747 chr22:29949763-29949772
25	POLR2A	chr22:29949400-29950175	K562	blood:	n/a	n/a
26	POLR2A	chr22:29949262-29950286	PANC-1	pancreas:	n/a	n/a
27	MTA3	chr22:29949135-29950353	GM12878	blood:	n/a	n/a
28	POLR2A	chr22:29949364-29950509	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr22:29949256-29950104	K562	blood:	n/a	n/a
30	POLR2A	chr22:29949461-29950018	GM10847	blood:	n/a	n/a
31	ELF1	chr22:29949311-29949994	GM12878	blood:	n/a	chr22:29949737-29949746 chr22:29949736-29949747
32	MAZ	chr22:29949311-29950036	GM12878	blood:	n/a	n/a
33	CEBPB	chr22:29949298-29950555	Hela-S3	cervix:	n/a	chr22:29950406-29950417
34	GABPA	chr22:29949509-29950058	Hela-S3	cervix:	n/a	n/a
35	NFIC	chr22:29949474-29950002	GM12878	blood:	n/a	n/a
36	POLR2A	chr22:29949504-29949996	A549	lung:	n/a	n/a
37	ETS1	chr22:29949470-29949951	K562	blood:	n/a	chr22:29949738-29949747 chr22:29949764-29949774 chr22:29949738-29949747 chr22:29949763-29949772 chr22:29949738-29949747 chr22:29949763-29949772 chr22:29949783-29949794 chr22:29949763-29949772 chr22:29949737-29949746 chr22:29949763-29949772 chr22:29949739-29949749 chr22:29949738-29949747 chr22:29949735-29949748 chr22:29949738-29949747 chr22:29949763-29949772 chr22:29949763-29949772 chr22:29949738-29949747 chr22:29949736-29949745 chr22:29949734-29949750 chr22:29949760-29949773 chr22:29949738-29949747
38	CCNT2	chr22:29949460-29949953	K562	blood:	n/a	n/a
39	POLR2A	chr22:29949323-29950516	HepG2	liver:	n/a	n/a
40	RCOR1	chr22:29949343-29950145	K562	blood:	n/a	n/a
41	POLR2A	chr22:29949305-29950011	GM12878	blood:	n/a	n/a
42	ELF1	chr22:29949297-29950211	HCT-116	colon:	n/a	chr22:29949737-29949746 chr22:29949736-29949747
43	MTA3	chr22:29949491-29950331	GM12878	blood:	n/a	n/a
44	MAX	chr22:29949266-29950384	HCT-116	colon:	n/a	chr22:29949844-29949854 chr22:29950270-29950277 chr22:29950268-29950281
45	MYC	chr22:29949329-29950069	H1-hESC	embryonic stem cell:	n/a	chr22:29949844-29949854
46	REST	chr22:29949426-29950359	HL-60	blood:	n/a	chr22:29949588-29949602
47	POLR2A	chr22:29949207-29950313	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr22:29949353-29950315	GM12892	blood:	n/a	n/a
49	MAX	chr22:29949376-29950320	K562	blood:	n/a	chr22:29949844-29949854 chr22:29950270-29950277 chr22:29950268-29950281
50	POLR2A	chr22:29949246-29950380	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29932048..29935657-chr22:29948099..29949813,3	MCF-7	breast:
2	chr22:29938209..29940408-chr22:29946980..29949798,2	K562	blood:
3	chr22:29948374..29951089-chr22:29975785..29978624,4	MCF-7	breast:
4	chr22:29947295..29951735-chr22:29976015..29980297,4	K562	blood:
5	chr22:29943855..29946022-chr22:29948104..29949862,2	K562	blood:
6	chr22:29948193..29950224-chr22:29975940..29978547,6	MCF-7	breast:
7	chr22:29938856..29940364-chr22:29948151..29949773,2	MCF-7	breast:
8	chr22:29940656..29942248-chr22:29948423..29951166,2	MCF-7	breast:

Variant related genes	Relation type
THOC5	TF binding region
ENSG00000100296	Chromatin interaction
ENSG00000184117	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs165602	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs165624	0.81[ASN][1000 genomes]
rs165734	0.81[ASN][1000 genomes]
rs165853	0.92[ASN][1000 genomes]
rs165899	0.81[ASN][1000 genomes]
rs1800540	0.85[ASN][1000 genomes]
rs2008880	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530660	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857634	0.85[ASN][1000 genomes]
rs457930	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467669	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs467768	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468563	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823046	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823048	0.85[ASN][1000 genomes]
rs5763315	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763347	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763348	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs695776	0.83[EUR][1000 genomes]
rs73159014	1.00[ASN][1000 genomes]
rs737979	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs469189	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29948400-29950800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr22:29948600-29949800	Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr22:29948600-29949800	Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr22:29948600-29950000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr22:29948600-29950000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr22:29948600-29950000	Active TSS	Fetal Brain Female	brain
7	chr22:29948600-29950000	Active TSS	HSMM	muscle
8	chr22:29948600-29950200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr22:29948600-29950200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr22:29948600-29950200	Active TSS	Brain Germinal Matrix	brain
11	chr22:29948600-29950200	Active TSS	Brain Hippocampus Middle	brain
12	chr22:29948600-29950200	Active TSS	A549	lung
13	chr22:29948600-29950400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr22:29948600-29950400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:29948600-29950400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr22:29948600-29950400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr22:29948600-29950400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr22:29948600-29950400	Active TSS	NHLF	lung
19	chr22:29948800-29950000	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr22:29948800-29950000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr22:29948800-29950000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr22:29948800-29950000	Active TSS	Primary T cells from cord blood	blood
23	chr22:29948800-29950000	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr22:29948800-29950000	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr22:29948800-29950000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr22:29948800-29950000	Active TSS	Muscle Satellite Cultured Cells	--
27	chr22:29948800-29950000	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr22:29948800-29950000	Active TSS	Fetal Intestine Small	intestine
29	chr22:29948800-29950000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr22:29948800-29950000	Active TSS	Hela-S3	cervix
31	chr22:29948800-29950000	Active TSS	HMEC	breast
32	chr22:29948800-29950000	Active TSS	HSMMtube	muscle
33	chr22:29948800-29950000	Active TSS	NH-A	brain
34	chr22:29948800-29950000	Active TSS	NHEK	skin
35	chr22:29948800-29950000	Active TSS	Osteobl	bone
36	chr22:29948800-29950200	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr22:29948800-29950200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:29948800-29950200	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr22:29948800-29950200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr22:29948800-29950200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr22:29948800-29950200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr22:29948800-29950200	Active TSS	Brain Angular Gyrus	brain
43	chr22:29948800-29950200	Active TSS	Brain Anterior Caudate	brain
44	chr22:29948800-29950200	Active TSS	Brain Cingulate Gyrus	brain
45	chr22:29948800-29950200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr22:29948800-29950200	Active TSS	Fetal Brain Male	brain
47	chr22:29948800-29950200	Active TSS	Rectal Smooth Muscle	rectum
48	chr22:29948800-29950200	Active TSS	GM12878-XiMat	blood
49	chr22:29948800-29950200	Active TSS	K562	blood
50	chr22:29948800-29950400	Active TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links