Variant report

Variant	rs41399845
Chromosome Location	chr19:43032607-43032608
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:60)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:60 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:43032455-43032698	GM12892	blood:	n/a	n/a
2	TAF1	chr19:43032345-43032741	HepG2	liver:	n/a	n/a
3	NFIC	chr19:43032422-43032958	GM12878	blood:	n/a	n/a
4	STAT3	chr19:43032550-43032860	MCF10A-Er-Src	breast:	n/a	chr19:43032738-43032749
5	POLR2A	chr19:43032499-43032660	A549	lung:	n/a	n/a
6	BHLHE40	chr19:43032441-43032956	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:43032502-43032903	HUVEC	blood vessel:	n/a	n/a
8	HEY1	chr19:43032316-43033163	HepG2	liver:	n/a	n/a
9	RAD21	chr19:43032489-43032819	HepG2	liver:	n/a	n/a
10	ELF1	chr19:43032451-43032914	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:43032429-43032680	GM12878	blood:	n/a	n/a
12	ELF1	chr19:43032363-43033854	GM12878	blood:	n/a	n/a
13	STAT1	chr19:43032439-43032905	GM12878	blood:	n/a	chr19:43032738-43032749
14	TAF1	chr19:43032404-43032735	HepG2	liver:	n/a	n/a
15	HEY1	chr19:43032428-43032813	HepG2	liver:	n/a	n/a
16	ELF1	chr19:43032412-43032812	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:43032434-43032864	HepG2	liver:	n/a	n/a
18	IKZF1	chr19:43032596-43033043	GM12878	blood:	n/a	n/a
19	ELF1	chr19:43032516-43032884	HepG2	liver:	n/a	n/a
20	RUNX3	chr19:43032504-43032994	GM12878	blood:	n/a	n/a
21	MYC	chr19:43032603-43032623	HepG2	liver:	n/a	n/a
22	TAF1	chr19:43032435-43032791	GM12878	blood:	n/a	n/a
23	CTCF	chr19:43031752-43034268	A549	lung:	n/a	chr19:43033585-43033603 chr19:43033591-43033600
24	SMC3	chr19:43032574-43032926	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:43032389-43033651	HepG2	liver:	n/a	n/a
26	MAZ	chr19:43032509-43032709	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:43032362-43032894	HepG2	liver:	n/a	n/a
28	POLR2A	chr19:43032363-43033285	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:43032387-43032716	HepG2	liver:	n/a	n/a
30	MAZ	chr19:43032467-43032987	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:43032444-43032678	GM12878	blood:	n/a	n/a
32	CHD2	chr19:43032516-43033740	GM12878	blood:	n/a	n/a
33	RFX5	chr19:43032499-43033032	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:43032385-43032684	GM12891	blood:	n/a	n/a
35	POLR2A	chr19:43032313-43033658	GM12891	blood:	n/a	n/a
36	TBP	chr19:43032437-43032897	HepG2	liver:	n/a	n/a
37	SMC3	chr19:43032420-43033878	GM12878	blood:	n/a	chr19:43032528-43032542
38	EBF1	chr19:43032425-43032962	GM12878	blood:	n/a	chr19:43032641-43032652
39	RAD21	chr19:43032465-43032911	HepG2	liver:	n/a	n/a
40	PML	chr19:43032317-43032894	GM12878	blood:	n/a	chr19:43032359-43032367
41	USF2	chr19:43032503-43032840	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:43032450-43032662	A549	lung:	n/a	n/a
43	POLR2A	chr19:43032318-43033643	HepG2	liver:	n/a	n/a
44	USF1	chr19:43032514-43032824	HepG2	liver:	n/a	n/a
45	POLR2A	chr19:43032389-43032844	GM12878	blood:	n/a	n/a
46	RUNX3	chr19:43032562-43033013	GM12878	blood:	n/a	n/a
47	CEBPD	chr19:43032382-43032707	HepG2	liver:	n/a	n/a
48	USF1	chr19:43032539-43032785	HepG2	liver:	n/a	n/a
49	MAFK	chr19:43032596-43032710	HepG2	liver:	n/a	n/a
50	POLR2A	chr19:43032392-43033005	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:43032587-43032637	SAEC	small airway:	n/a
2	chr19:43032587-43032637	IMR90	lung:	fetal
3	chr19:43032587-43032637	NHBE	bronchial:	n/a
4	chr19:43032587-43032637	NH-A	brain:	n/a
5	chr19:43032587-43032637	K562	blood:	n/a
6	chr19:43032587-43032637	BE2_C	brain:	n/a
7	chr19:43032587-43032637	ovcar-3	ovarian:	n/a
8	chr19:43032587-43032637	HCT-116	colon:	n/a
9	chr19:43032587-43032637	PFSK-1	brain:	n/a
10	chr19:43032587-43032637	GM06990	blood:	n/a
11	chr19:43032587-43032637	SK-N-MC	brain:	n/a
12	chr19:43032587-43032637	RPTEC	kidney:	n/a
13	chr19:43032587-43032637	Hepatocyte	liver:	n/a
14	chr19:43032587-43032637	Jurkat	blood:	n/a
15	chr19:43032587-43032637	H1-hESC	embryonic stem cell:	embryo
16	chr19:43032587-43032637	AG04449	skin:	fetal
17	chr19:43032587-43032637	AG09319	gingival:	n/a
18	chr19:43032587-43032637	HRPEpiC	eye:	n/a
19	chr19:43032587-43032637	HL-60	blood:	n/a
20	chr19:43032587-43032637	AG09309	skin:	n/a
21	chr19:43032587-43032637	MCF-7	breast:	n/a
22	chr19:43032587-43032637	A549	lung:	n/a
23	chr19:43032587-43032637	HIPEpiC	eye:	n/a
24	chr19:43032587-43032637	GM12892	blood:	n/a
25	chr19:43032587-43032637	Hela-S3	cervix:	n/a
26	chr19:43032587-43032637	MCF10A-Er-Src	breast:	n/a
27	chr19:43032587-43032637	SK-N-SH_RA	brain:	n/a
28	chr19:43032587-43032637	GM12891	blood:	n/a
29	chr19:43032587-43032637	HAEpiC	amniotic membrane:	n/a
30	chr19:43032587-43032637	AG04450	lung:	fetal
31	chr19:43032587-43032637	GM19239	blood:	n/a
32	chr19:43032587-43032637	HepG2	liver:	n/a
33	chr19:43032587-43032637	AG10803	skin:	n/a
34	chr19:43032587-43032637	HEK293	kidney:	embryo
35	chr19:43032587-43032637	ProgFib	skin:	n/a
36	chr19:43032587-43032637	SKMC	muscle:	n/a
37	chr19:43032587-43032637	NT2-D1	testis:	n/a
38	chr19:43032587-43032637	SK-N-SH	brain:	n/a
39	chr19:43032587-43032637	NB4	blood:	n/a
40	chr19:43032587-43032637	ECC-1	luminal epithelium:	n/a
41	chr19:43032587-43032637	HUVEC	blood vessel:	n/a
42	chr19:43032587-43032637	HCF	heart:	n/a
43	chr19:43032587-43032637	BJ	skin:	n/a
44	chr19:43032587-43032637	U87	brain:	n/a
45	chr19:43032587-43032637	Caco-2	colon:	n/a
46	chr19:43032587-43032637	HCPEpiC	choroid plexus:	n/a
47	chr19:43032587-43032637	HPAEpiC	pulmonary alveolar:	n/a
48	chr19:43032587-43032637	T-47D	breast:	n/a
49	chr19:43032587-43032637	AoSMC	blood vessel:	n/a
50	chr19:43032587-43032637	GM12878	blood:	n/a

No data

Variant related genes	Relation type
CEACAM1	TF binding region
CEACAM1	CpG island

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16975752	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975764	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16980938	1.00[AMR][1000 genomes]
rs41370146	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41446950	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41454446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs45503698	0.83[AFR][1000 genomes]
rs45517531	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs45542933	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs45600939	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8103049	0.84[AFR][1000 genomes]
rs8110553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2422468	chr19:42991289-43669027	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1057390	chr19:43003323-43173028	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43023600-43033200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:43026200-43032800	Weak transcription	Fetal Stomach	stomach
3	chr19:43030400-43033000	Active TSS	Esophagus	oesophagus
4	chr19:43030400-43033000	Active TSS	Sigmoid Colon	Sigmoid Colon
5	chr19:43030400-43033400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr19:43030400-43033600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr19:43030400-43033600	Active TSS	Rectal Smooth Muscle	rectum
8	chr19:43030800-43032800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr19:43031000-43033600	Enhancers	Spleen	Spleen
10	chr19:43031200-43033600	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr19:43031400-43033600	Flanking Active TSS	Liver	Liver
12	chr19:43031600-43033600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:43031600-43033600	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr19:43031600-43033600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr19:43031800-43033600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:43032000-43033400	Enhancers	Brain Cingulate Gyrus	brain
17	chr19:43032000-43033400	Enhancers	A549	lung
18	chr19:43032000-43033600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr19:43032000-43033600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr19:43032000-43033600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr19:43032000-43033600	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr19:43032000-43033600	Enhancers	Fetal Muscle Leg	muscle
23	chr19:43032000-43033600	Enhancers	Gastric	stomach
24	chr19:43032000-43033800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr19:43032200-43032800	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr19:43032200-43032800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:43032200-43032800	Active TSS	Brain Hippocampus Middle	brain
28	chr19:43032200-43033000	Active TSS	Right Atrium	heart
29	chr19:43032200-43033200	Active TSS	Small Intestine	intestine
30	chr19:43032200-43033400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:43032200-43033400	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr19:43032200-43033600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr19:43032200-43033600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:43032200-43033600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:43032200-43033600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:43032200-43033600	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr19:43032200-43033600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr19:43032200-43033600	Flanking Active TSS	GM12878-XiMat	blood
39	chr19:43032200-43033800	Enhancers	Lung	lung
40	chr19:43032400-43032800	Enhancers	Brain Anterior Caudate	brain
41	chr19:43032400-43032800	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr19:43032400-43032800	Active TSS	Right Ventricle	heart
43	chr19:43032400-43033000	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr19:43032400-43033000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr19:43032400-43033000	Enhancers	Brain Substantia Nigra	brain
46	chr19:43032400-43033200	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr19:43032400-43033200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:43032400-43033200	Active TSS	HepG2	liver
49	chr19:43032400-43033200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr19:43032400-43033200	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links