Variant report

Variant	rs390134
Chromosome Location	chr19:44454973-44454974
allele	A/C
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	ELF1	chr19:44454895-44455818	HCT-116	colon:	n/a	chr19:44455330-44455343
2	MAX	chr19:44454963-44455509	ECC-1	luminal epithelium:	n/a	n/a
3	HCFC1	chr19:44454847-44455986	Hela-S3	cervix:	n/a	n/a
4	ELF1	chr19:44454956-44455750	MCF-7	breast:	n/a	chr19:44455330-44455343
5	EP300	chr19:44454872-44455549	A549	lung:	n/a	chr19:44455332-44455339
6	CEBPB	chr19:44454934-44455524	GM12878	blood:	n/a	n/a
7	MAZ	chr19:44454884-44455822	IMR90	lung:	n/a	n/a
8	BCL3	chr19:44454856-44455743	A549	lung:	n/a	chr19:44455331-44455340 chr19:44455584-44455597
9	CTCF	chr19:44454941-44455472	K562	blood:	n/a	chr19:44455243-44455264 chr19:44455254-44455263 chr19:44455248-44455266
10	SP1	chr19:44454934-44455719	A549	lung:	n/a	n/a
11	CBX3	chr19:44454852-44455721	K562	blood:	n/a	n/a
12	CEBPB	chr19:44454952-44455518	ECC-1	luminal epithelium:	n/a	n/a
13	GABPA	chr19:44454958-44455743	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:44454923-44455708	HUVEC	blood vessel:	n/a	n/a
15	TEAD4	chr19:44454879-44455541	K562	blood:	n/a	n/a
16	GABPA	chr19:44454966-44455676	HL-60	blood:	n/a	n/a
17	POLR2A	chr19:44454966-44455461	SK-N-MC	brain:	n/a	n/a
18	CEBPB	chr19:44454893-44455613	HCT-116	colon:	n/a	n/a
19	MAX	chr19:44454955-44455616	ECC-1	luminal epithelium:	n/a	n/a
20	CBX3	chr19:44454958-44455460	K562	blood:	n/a	n/a
21	ARID3A	chr19:44454922-44455472	K562	blood:	n/a	n/a
22	REST	chr19:44454924-44456075	H1-neurons	neurons:	n/a	n/a
23	MAX	chr19:44454959-44455827	A549	lung:	n/a	n/a
24	GABPA	chr19:44454902-44455804	A549	lung:	n/a	n/a
25	TCF12	chr19:44454794-44455825	A549	lung:	n/a	n/a
26	CEBPB	chr19:44454838-44455708	HCT-116	colon:	n/a	n/a
27	ELF1	chr19:44454966-44455681	SK-N-SH	brain:	n/a	chr19:44455330-44455343
28	TBP	chr19:44454897-44455564	GM12878	blood:	n/a	n/a
29	SP1	chr19:44454901-44455645	A549	lung:	n/a	n/a
30	YY1	chr19:44454967-44455539	SK-N-SH_RA	brain:	n/a	chr19:44455154-44455170
31	MAX	chr19:44454879-44455900	A549	lung:	n/a	n/a
32	CEBPB	chr19:44454915-44455518	MCF-7	breast:	n/a	n/a
33	CEBPB	chr19:44454966-44455497	K562	blood:	n/a	n/a
34	GATA3	chr19:44454821-44455745	A549	lung:	n/a	chr19:44455522-44455532 chr19:44455020-44455028
35	ZBTB33	chr19:44454938-44455514	A549	lung:	n/a	chr19:44455394-44455404
36	ELF1	chr19:44454965-44455788	HCT-116	colon:	n/a	chr19:44455330-44455343
37	BCL3	chr19:44454871-44455629	A549	lung:	n/a	chr19:44455331-44455340 chr19:44455584-44455597
38	SIX5	chr19:44454771-44455785	A549	lung:	n/a	chr19:44455366-44455375 chr19:44455368-44455377 chr19:44455365-44455379
39	REST	chr19:44454926-44455724	A549	lung:	n/a	n/a
40	GABPA	chr19:44454833-44455823	A549	lung:	n/a	n/a
41	CEBPB	chr19:44454833-44455624	A549	lung:	n/a	n/a
42	POLR2A	chr19:44454962-44455516	HUVEC	blood vessel:	n/a	n/a
43	CEBPB	chr19:44454963-44455476	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr19:44454942-44455655	SK-N-SH	brain:	n/a	n/a
45	GABPA	chr19:44454884-44455739	HL-60	blood:	n/a	n/a
46	RUNX3	chr19:44454921-44455564	GM12878	blood:	n/a	n/a
47	CEBPB	chr19:44454947-44455539	A549	lung:	n/a	n/a
48	RAD21	chr19:44454958-44455550	MCF-7	breast:	n/a	chr19:44455246-44455265
49	GABPA	chr19:44454882-44455823	SK-N-SH	brain:	n/a	n/a
50	GABPA	chr19:44454852-44456007	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44439254..44441098-chr19:44452141..44456291,4	K562	blood:

Variant related genes	Relation type
ZNF221	TF binding region
ENSG00000124459	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10402944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299936	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429734	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs366431	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs368492	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs376655	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377931	0.84[EUR][1000 genomes]
rs377934	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381220	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs381872	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs385202	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs385578	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs386249	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs386747	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs388547	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs391961	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs394132	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs394380	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395419	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs396188	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs400591	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs401770	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs413061	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs415468	0.90[EUR][1000 genomes]
rs415867	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs424041	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs427401	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs429611	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs437700	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs439417	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs441386	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs441742	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs442543	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs444816	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs445865	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs453682	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs454376	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers 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	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44453400-44455000	Weak transcription	Esophagus	oesophagus
2	chr19:44453400-44455200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:44453400-44455200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:44453600-44455000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:44453600-44455200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:44453600-44455200	Weak transcription	Pancreas	Pancrea
7	chr19:44454400-44456000	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr19:44454800-44455000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr19:44454800-44455000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr19:44454800-44455000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr19:44454800-44455000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr19:44454800-44455000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr19:44454800-44455000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:44454800-44455000	Active TSS	Adipose Nuclei	Adipose
15	chr19:44454800-44455000	Enhancers	Hela-S3	cervix
16	chr19:44454800-44455200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr19:44454800-44455200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:44454800-44455200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:44454800-44455400	Active TSS	Primary B cells from cord blood	blood
20	chr19:44454800-44455400	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr19:44454800-44455600	Active TSS	Primary hematopoietic stem cells	blood
22	chr19:44454800-44455600	Active TSS	Liver	Liver
23	chr19:44454800-44455600	Active TSS	Monocytes-CD14+_RO01746	blood
24	chr19:44454800-44455800	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr19:44454800-44456000	Active TSS	Colonic Mucosa	Colon
26	chr19:44454800-44456000	Active TSS	Duodenum Mucosa	Duodenum
27	chr19:44454800-44456000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr19:44454800-44456000	Active TSS	A549	lung
29	chr19:44454800-44456000	Active TSS	GM12878-XiMat	blood
30	chr19:44454800-44456000	Active TSS	K562	blood
31	chr19:44454800-44456000	Active TSS	NHEK	skin
32	chr19:44454800-44456200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:44454800-44456200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:44454800-44456200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:44454800-44456200	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr19:44454800-44456400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:44454800-44456400	Active TSS	Brain Anterior Caudate	brain
38	chr19:44454800-44456400	Active TSS	Brain Hippocampus Middle	brain
39	chr19:44454800-44456400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:44454800-44456400	Active TSS	HMEC	breast
41	chr19:44454800-44456600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr19:44454800-44456600	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr19:44454800-44456600	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr19:44454800-44456600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:44454800-44456600	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr19:44454800-44456600	Active TSS	Rectal Smooth Muscle	rectum
47	chr19:44454800-44456600	Flanking Active TSS	Dnd41	blood
48	chr19:44454800-44456600	Active TSS	HUVEC	blood vessel
49	chr19:44454800-44456800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr19:44454800-44456800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links