Variant report

Variant	rs884480
Chromosome Location	chr19:19773923-19773924
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	PAX5	chr19:19773848-19774239	GM12878	blood:	n/a	n/a
2	ELK1	chr19:19773814-19774874	GM12878	blood:	n/a	chr19:19774531-19774540 chr19:19774531-19774540
3	POLR2A	chr19:19773478-19774877	PBDE	blood:	n/a	n/a
4	MYC	chr19:19773784-19775113	K562	blood:	n/a	chr19:19774771-19774780 chr19:19774581-19774590
5	POLR2A	chr19:19772031-19775125	GM19193	blood:	n/a	n/a
6	JUN	chr19:19773633-19773942	K562	blood:	n/a	chr19:19773873-19773882
7	SMC3	chr19:19773775-19774146	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:19773754-19775152	K562	blood:	n/a	n/a
9	MAX	chr19:19773832-19774295	A549	lung:	n/a	n/a
10	YY1	chr19:19773774-19775206	SK-N-SH	brain:	n/a	chr19:19774467-19774479 chr19:19774543-19774557
11	POLR2A	chr19:19773885-19775092	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr19:19772640-19775184	Raji	blood:	n/a	n/a
13	POLR2A	chr19:19771886-19774863	GM12878	blood:	n/a	n/a
14	CREB1	chr19:19773767-19775141	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:19772026-19775170	GM18505	blood:	n/a	n/a
16	POLR2A	chr19:19772545-19775164	GM18526	blood:	n/a	n/a
17	REST	chr19:19773864-19774897	HL-60	blood:	n/a	n/a
18	POLR2A	chr19:19772089-19775169	GM18951	blood:	n/a	n/a
19	POLR2A	chr19:19772425-19775227	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr19:19772506-19775176	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:19771866-19775239	GM12892	blood:	n/a	n/a
22	NRF1	chr19:19773914-19774845	GM12878	blood:	n/a	chr19:19774138-19774149
23	TCF3	chr19:19773858-19775014	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:19773875-19774870	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr19:19773879-19775037	MCF-7	breast:	n/a	chr19:19774771-19774780 chr19:19774581-19774590
26	CTCF	chr19:19773900-19774050	HRPEpiC	eye:	n/a	n/a
27	MXI1	chr19:19771963-19775426	SK-N-SH	brain:	n/a	chr19:19774765-19774780 chr19:19774550-19774565
28	GABPA	chr19:19773803-19775137	K562	blood:	n/a	n/a
29	HCFC1	chr19:19773629-19775264	Hela-S3	cervix:	n/a	n/a
30	MXI1	chr19:19773724-19774935	K562	blood:	n/a	chr19:19774765-19774780 chr19:19774550-19774565
31	WRNIP1	chr19:19772134-19774816	GM12878	blood:	n/a	n/a
32	EBF1	chr19:19773909-19774885	GM12878	blood:	n/a	n/a
33	MYC	chr19:19773735-19774997	K562	blood:	n/a	chr19:19774771-19774780 chr19:19774581-19774590
34	BCLAF1	chr19:19773791-19774868	GM12878	blood:	n/a	chr19:19774531-19774540 chr19:19774494-19774503 chr19:19774707-19774716
35	POLR2A	chr19:19773908-19774856	MCF-7	breast:	n/a	n/a
36	POLR2A	chr19:19773854-19775177	NB4	blood:	n/a	n/a
37	POLR2A	chr19:19771901-19775139	K562	blood:	n/a	n/a
38	CREB1	chr19:19773705-19774981	K562	blood:	n/a	n/a
39	POLR2A	chr19:19772159-19775226	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:19772681-19774998	HepG2	liver:	n/a	n/a
41	MXI1	chr19:19773761-19774955	GM12878	blood:	n/a	chr19:19774765-19774780 chr19:19774550-19774565
42	POU2F2	chr19:19773609-19774888	GM12878	blood:	n/a	n/a
43	YY1	chr19:19773757-19775090	HepG2	liver:	n/a	chr19:19774467-19774479 chr19:19774543-19774557
44	MYC	chr19:19773897-19774858	MCF-7	breast:	n/a	chr19:19774771-19774780 chr19:19774581-19774590
45	UBTF	chr19:19773594-19774808	K562	blood:	n/a	n/a
46	POLR2A	chr19:19771894-19774978	GM12891	blood:	n/a	n/a
47	YY1	chr19:19773840-19774999	GM12892	blood:	n/a	chr19:19774467-19774479 chr19:19774543-19774557
48	POLR2A	chr19:19772531-19774868	GM12891	blood:	n/a	n/a
49	TBP	chr19:19773917-19775188	K562	blood:	n/a	n/a
50	POLR2A	chr19:19773858-19774887	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19625322..19628012-chr19:19773852..19776193,2	K562	blood:
2	chr19:19625773..19627404-chr19:19772860..19774540,2	MCF-7	breast:
3	chr19:19755704..19761642-chr19:19771468..19774473,6	MCF-7	breast:
4	chr19:19748686..19750462-chr19:19773488..19775987,2	K562	blood:
5	chr19:19753534..19755355-chr19:19771479..19774786,3	MCF-7	breast:
6	chr19:19623259..19625867-chr19:19772617..19774685,2	MCF-7	breast:
7	chr19:19739216..19741548-chr19:19773041..19775101,2	K562	blood:
8	chr19:19647870..19650487-chr19:19773815..19776020,2	MCF-7	breast:
9	chr1:28974889..28975516-chr19:19773844..19774668,2	Hela-S3	cervix:
10	chr19:19748686..19750462-chr19:19772850..19775987,3	K562	blood:
11	chr19:19636166..19641062-chr19:19772143..19775843,4	MCF-7	breast:
12	chr19:19751259..19757786-chr19:19771999..19776232,8	K562	blood:
13	chr19:19649331..19652417-chr19:19771491..19776120,6	K562	blood:
14	chr19:19729417..19731495-chr19:19772370..19774542,2	MCF-7	breast:
15	chr19:19767560..19771032-chr19:19771876..19774701,8	MCF-7	breast:
16	chr19:19649600..19655493-chr19:19770960..19774805,7	K562	blood:
17	chr19:19751259..19758144-chr19:19770384..19776332,14	K562	blood:
18	chr19:19772600..19774395-chr19:19886060..19888388,2	MCF-7	breast:
19	chr19:19772731..19775725-chr19:19841970..19845590,5	MCF-7	breast:
20	chr19:19673046..19675875-chr19:19772243..19774932,2	K562	blood:
21	chr19:19772622..19775616-chr19:19842700..19844547,2	MCF-7	breast:
22	chr19:19772164..19776257-chr19:19777737..19781997,10	MCF-7	breast:
23	chr19:19752144..19756505-chr19:19773208..19775858,7	MCF-7	breast:

Variant related genes	Relation type
ATP13A1	TF binding region
ENSG00000089639	Chromatin interaction
ENSG00000105708	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000105717	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000181896	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000266904	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000267419	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10401926	1.00[CEU][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10403579	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10415278	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10421328	0.88[CEU][hapmap];0.84[MEX][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs10423449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11668721	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11671684	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2288865	0.88[CEU][hapmap];0.80[TSI][hapmap];0.87[YRI][hapmap]
rs2288867	0.83[CEU][hapmap]
rs34174818	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56236407	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7253821	0.94[CEU][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73006705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs867616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs919778	0.88[CEU][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs884480	GMIP	cis	parietal	SCAN
rs884480	C21orf128	trans	cerebellum	SCAN
rs884480	ZNF101	cis	parietal	SCAN
rs884480	C19orf60	cis	parietal	SCAN
rs884480	SNORA68	cis	parietal	SCAN
rs884480	ZNF714	cis	parietal	SCAN
rs884480	MED26	cis	parietal	SCAN
rs884480	ZNF14	cis	cerebellum	SCAN
rs884480	ZNF14	cis	parietal	SCAN
rs884480	OCEL1	cis	parietal	SCAN
rs884480	UNC13A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19772000-19774000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr19:19772000-19774000	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr19:19772000-19774400	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr19:19772200-19774200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr19:19772400-19774000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:19772400-19774000	Flanking Active TSS	Fetal Brain Female	brain
7	chr19:19772400-19774200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:19772600-19774000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:19772600-19774200	Flanking Active TSS	Primary B cells from peripheral blood	blood
10	chr19:19772600-19774200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:19772600-19775400	Active TSS	GM12878-XiMat	blood
12	chr19:19772800-19774200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr19:19772800-19774200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr19:19772800-19774200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr19:19772800-19774400	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:19773000-19774000	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr19:19773000-19774000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr19:19773000-19774000	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr19:19773000-19774000	Flanking Active TSS	Fetal Thymus	thymus
20	chr19:19773000-19774000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr19:19773000-19774000	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr19:19773000-19774000	Flanking Active TSS	NH-A	brain
23	chr19:19773000-19774000	Flanking Active TSS	NHLF	lung
24	chr19:19773000-19774200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr19:19773000-19774200	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr19:19773000-19774200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:19773000-19774200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr19:19773000-19774200	Flanking Active TSS	Liver	Liver
29	chr19:19773000-19774200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr19:19773000-19774400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
31	chr19:19773200-19774000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:19773200-19774000	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr19:19773200-19774000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr19:19773200-19774000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:19773200-19774000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:19773200-19774000	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr19:19773200-19774000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:19773200-19774000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr19:19773200-19774000	Flanking Active TSS	Fetal Lung	lung
40	chr19:19773200-19774000	Flanking Active TSS	Pancreas	Pancrea
41	chr19:19773200-19774000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr19:19773200-19774200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr19:19773200-19774200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr19:19773200-19774200	Flanking Active TSS	Colonic Mucosa	Colon
45	chr19:19773200-19774200	Flanking Active TSS	Right Ventricle	heart
46	chr19:19773200-19774200	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr19:19773200-19775200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:19773200-19775200	Active TSS	Fetal Kidney	kidney
49	chr19:19773400-19774000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:19773400-19774000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links