Variant report

Variant	rs1233444
Chromosome Location	chr19:44764064-44764065
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	FOXA1	chr19:44763900-44764205	T-47D	breast:	n/a	n/a
2	HEY1	chr19:44763846-44764341	HepG2	liver:	n/a	n/a
3	CHD2	chr19:44763888-44764225	Hela-S3	cervix:	n/a	n/a
4	SIX5	chr19:44763805-44764233	A549	lung:	n/a	n/a
5	YY1	chr19:44763864-44764358	SK-N-SH_RA	brain:	n/a	n/a
6	GABPA	chr19:44763795-44764422	A549	lung:	n/a	n/a
7	RCOR1	chr19:44763795-44764754	IMR90	lung:	n/a	n/a
8	PAX5	chr19:44763822-44764265	GM12878	blood:	n/a	n/a
9	SIX5	chr19:44763768-44764214	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr19:44763927-44764612	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:44763794-44764256	PANC-1	pancreas:	n/a	n/a
12	MAX	chr19:44763990-44764320	GM12878	blood:	n/a	n/a
13	TBP	chr19:44763939-44764233	Hela-S3	cervix:	n/a	n/a
14	TBP	chr19:44764004-44764175	K562	blood:	n/a	n/a
15	JUND	chr19:44763862-44764372	MCF-7	breast:	n/a	chr19:44764090-44764101
16	MAX	chr19:44763789-44764446	MCF-7	breast:	n/a	n/a
17	POLR2A	chr19:44763828-44764286	Hela-S3	cervix:	n/a	n/a
18	YY1	chr19:44763836-44764232	HepG2	liver:	n/a	n/a
19	HCFC1	chr19:44763824-44764199	K562	blood:	n/a	n/a
20	FOSL1	chr19:44763856-44764254	K562	blood:	n/a	chr19:44764090-44764101
21	ELF1	chr19:44763806-44764391	A549	lung:	n/a	chr19:44764188-44764200 chr19:44764041-44764054
22	ETS1	chr19:44763877-44764197	K562	blood:	n/a	n/a
23	MAZ	chr19:44763935-44764176	K562	blood:	n/a	n/a
24	POLR2A	chr19:44763840-44764255	A549	lung:	n/a	n/a
25	GABPA	chr19:44763799-44764296	Hela-S3	cervix:	n/a	n/a
26	ELF1	chr19:44763900-44764139	HepG2	liver:	n/a	chr19:44764041-44764054
27	FOS	chr19:44763965-44764220	MCF10A-Er-Src	breast:	n/a	chr19:44764090-44764101
28	TAF1	chr19:44763944-44764288	H1-neurons	neurons:	n/a	n/a
29	SIX5	chr19:44763853-44764112	GM12878	blood:	n/a	n/a
30	GABPA	chr19:44763666-44764327	K562	blood:	n/a	n/a
31	SIX5	chr19:44763859-44764138	K562	blood:	n/a	n/a
32	KAP1	chr19:44763912-44764433	HEK293	kidney:	n/a	n/a
33	POLR2A	chr19:44763821-44764390	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:44763816-44764420	MCF-7	breast:	n/a	n/a
35	POLR2A	chr19:44763770-44764442	Hela-S3	cervix:	n/a	n/a
36	MYC	chr19:44763965-44764205	K562	blood:	n/a	n/a
37	SPI1	chr19:44763869-44764274	GM12878	blood:	n/a	n/a
38	MXI1	chr19:44763887-44764241	HepG2	liver:	n/a	n/a
39	TAF1	chr19:44763938-44764211	SK-N-SH	brain:	n/a	n/a
40	FOSL2	chr19:44763873-44764278	HepG2	liver:	n/a	chr19:44764089-44764100
41	SPI1	chr19:44763884-44764271	GM12891	blood:	n/a	n/a
42	MAX	chr19:44763877-44764250	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr19:44763819-44764386	MCF-7	breast:	n/a	n/a
44	POLR2A	chr19:44763859-44764280	Hela-S3	cervix:	n/a	n/a
45	ELF1	chr19:44763851-44764229	K562	blood:	n/a	chr19:44764188-44764200 chr19:44764041-44764054
46	POLR2A	chr19:44763829-44764359	HL-60	blood:	n/a	n/a
47	POLR2A	chr19:44763865-44764321	GM12891	blood:	n/a	n/a
48	JUND	chr19:44763926-44764251	HepG2	liver:	n/a	chr19:44764090-44764101
49	FOS	chr19:44763927-44764329	HUVEC	blood vessel:	n/a	chr19:44764090-44764101
50	FOXA1	chr19:44763854-44764138	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44763153..44765827-chr19:44767005..44769957,2	MCF-7	breast:
2	chr19:44762662..44765169-chr19:44806024..44808707,2	K562	blood:
3	chr19:44763689..44765733-chr19:44807177..44810075,2	MCF-7	breast:
4	chr19:44763704..44764619-chr3:149095039..149095904,2	Hela-S3	cervix:
5	chr19:44763163..44765702-chr19:44978103..44979674,2	MCF-7	breast:

Variant related genes	Relation type
ZNF233	TF binding region
ENSG00000240541	Chromatin interaction
ENSG00000159917	Chromatin interaction
ENSG00000267242	Chromatin interaction
ENSG00000169908	Chromatin interaction
ENSG00000159915	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1233428	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233441	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233447	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233459	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233466	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233467	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233468	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233470	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974099	0.88[ASN][1000 genomes]
rs1434574	0.85[ASN][1000 genomes]
rs1582	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1808735	0.86[ASN][1000 genomes]
rs1821458	0.86[ASN][1000 genomes]
rs1821459	0.86[ASN][1000 genomes]
rs2571062	0.84[ASN][1000 genomes]
rs2571099	0.84[ASN][1000 genomes]
rs2571101	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2571102	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2571104	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs2609874	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609875	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2609877	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2609880	0.86[ASN][1000 genomes]
rs2609894	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2609895	0.88[ASN][1000 genomes]
rs2609896	0.88[ASN][1000 genomes]
rs2609897	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2609908	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2722714	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2722720	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2722722	0.86[ASN][1000 genomes]
rs2722723	0.86[ASN][1000 genomes]
rs2722725	0.86[ASN][1000 genomes]
rs2722726	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2722727	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2722731	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2722737	0.84[ASN][1000 genomes]
rs2722740	0.82[CEU][hapmap]
rs2722751	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280359	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4325673	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4640292	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802216	0.87[CEU][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7249559	0.88[ASN][1000 genomes]
rs892595	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521923	chr19:44764064-44769974	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1233444	DMPK	cis	parietal	SCAN
rs1233444	KPTN	cis	cerebellum	SCAN
rs1233444	FPR3	cis	cerebellum	SCAN
rs1233444	ZNF233	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44729800-44768600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:44730000-44775600	ZNF genes & repeats	Liver	Liver
3	chr19:44763200-44764400	Active TSS	Primary hematopoietic stem cells	blood
4	chr19:44763200-44764800	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr19:44763400-44764400	Active TSS	A549	lung
6	chr19:44763400-44764600	Active TSS	Brain Substantia Nigra	brain
7	chr19:44763400-44764600	Active TSS	Colon Smooth Muscle	Colon
8	chr19:44763400-44764800	Active TSS	Brain Angular Gyrus	brain
9	chr19:44763400-44765400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr19:44763600-44764200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:44763600-44764200	Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr19:44763600-44764200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:44763600-44764200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:44763600-44764200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:44763600-44764200	Active TSS	Dnd41	blood
16	chr19:44763600-44764200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr19:44763600-44764200	Active TSS	NHEK	skin
18	chr19:44763600-44764400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:44763600-44764400	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr19:44763600-44764400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:44763600-44764400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:44763600-44764400	Active TSS	Fetal Brain Female	brain
23	chr19:44763600-44764600	Active TSS	Brain Germinal Matrix	brain
24	chr19:44763600-44764600	Active TSS	Fetal Intestine Large	intestine
25	chr19:44763600-44764600	Active TSS	Fetal Intestine Small	intestine
26	chr19:44763600-44764600	Active TSS	Fetal Lung	lung
27	chr19:44763600-44764800	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr19:44763600-44764800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:44763600-44764800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:44763600-44764800	Active TSS	Right Ventricle	heart
31	chr19:44763600-44765000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr19:44763600-44765000	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:44763600-44765000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:44763600-44765000	Active TSS	Brain Hippocampus Middle	brain
35	chr19:44763600-44765200	Active TSS	Duodenum Mucosa	Duodenum
36	chr19:44763800-44764200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:44763800-44764200	Active TSS	Fetal Thymus	thymus
38	chr19:44763800-44764200	Active TSS	Hela-S3	cervix
39	chr19:44763800-44764200	Active TSS	HUVEC	blood vessel
40	chr19:44763800-44764200	Active TSS	K562	blood
41	chr19:44763800-44764200	Active TSS	NHDF-Ad	bronchial
42	chr19:44763800-44764200	Active TSS	Osteobl	bone
43	chr19:44763800-44764400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:44763800-44764400	Active TSS	Primary T cells from cord blood	blood
45	chr19:44763800-44764400	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr19:44763800-44764400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr19:44763800-44764400	Active TSS	Fetal Muscle Trunk	muscle
48	chr19:44763800-44764400	Active TSS	Fetal Muscle Leg	muscle
49	chr19:44763800-44764400	Active TSS	Fetal Stomach	stomach
50	chr19:44763800-44764400	Active TSS	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links