Variant report

Variant	rs3745958
Chromosome Location	chr19:38893924-38893925
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	YY1	chr19:38893117-38894435	K562	blood:	n/a	chr19:38893702-38893716 chr19:38893945-38893954
2	EBF1	chr19:38893774-38893985	GM12878	blood:	n/a	n/a
3	BHLHE40	chr19:38893483-38894036	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:38893619-38894499	HL-60	blood:	n/a	n/a
5	CTCF	chr19:38893103-38894443	SK-N-SH	brain:	n/a	chr19:38893765-38893775 chr19:38893763-38893772 chr19:38893763-38893776 chr19:38893947-38893960 chr19:38893763-38893776 chr19:38893760-38893778 chr19:38893904-38893917 chr19:38893761-38893777 chr19:38893569-38893579
6	CREB1	chr19:38893223-38894059	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr19:38893341-38894362	A549	lung:	n/a	chr19:38894146-38894156 chr19:38893956-38893966 chr19:38893946-38893956 chr19:38894160-38894169
8	RAD21	chr19:38893320-38893990	HepG2	liver:	n/a	chr19:38893904-38893914 chr19:38893766-38893776 chr19:38893902-38893914 chr19:38893761-38893780
9	NR2F2	chr19:38893636-38893939	K562	blood:	n/a	n/a
10	POLR2A	chr19:38893368-38894135	Hela-S3	cervix:	n/a	n/a
11	RAD21	chr19:38893314-38893983	HepG2	liver:	n/a	chr19:38893904-38893914 chr19:38893766-38893776 chr19:38893902-38893914 chr19:38893761-38893780
12	MYC	chr19:38893344-38894406	K562	blood:	n/a	chr19:38894146-38894156 chr19:38893956-38893966 chr19:38893946-38893956 chr19:38894160-38894169
13	GABPA	chr19:38893550-38893990	H1-hESC	embryonic stem cell:	n/a	chr19:38893945-38893954 chr19:38893728-38893737
14	EP300	chr19:38893338-38893981	K562	blood:	n/a	chr19:38893947-38893963
15	ATF3	chr19:38893164-38893988	A549	lung:	n/a	chr19:38893945-38893954
16	TAF1	chr19:38893700-38893935	GM12878	blood:	n/a	n/a
17	RAD21	chr19:38893234-38894074	A549	lung:	n/a	chr19:38893904-38893914 chr19:38893766-38893776 chr19:38893902-38893914 chr19:38893761-38893780
18	REST	chr19:38893208-38894484	A549	lung:	n/a	chr19:38893565-38893575 chr19:38893873-38893886 chr19:38893889-38893902
19	POLR2A	chr19:38893326-38894060	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr19:38893817-38894005	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXP2	chr19:38893509-38894361	PFSK-1	brain:	n/a	n/a
22	CTCF	chr19:38893409-38893954	GM12878	blood:	n/a	chr19:38893765-38893775 chr19:38893763-38893772 chr19:38893763-38893776 chr19:38893763-38893776 chr19:38893760-38893778 chr19:38893904-38893917 chr19:38893761-38893777 chr19:38893569-38893579
23	YY1	chr19:38893284-38893942	H1-hESC	embryonic stem cell:	n/a	chr19:38893702-38893716
24	TAF1	chr19:38893607-38894085	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr19:38893369-38894012	IMR90	lung:	n/a	chr19:38893765-38893775 chr19:38893763-38893772 chr19:38893763-38893776 chr19:38893947-38893960 chr19:38893763-38893776 chr19:38893760-38893778 chr19:38893904-38893917 chr19:38893761-38893777 chr19:38893569-38893579
26	MAX	chr19:38893300-38894515	K562	blood:	n/a	chr19:38894146-38894156 chr19:38893956-38893966 chr19:38893946-38893956 chr19:38894160-38894169
27	TCF7L2	chr19:38893254-38894172	HCT-116	colon:	n/a	n/a
28	CTCF	chr19:38893318-38893980	HepG2	liver:	n/a	chr19:38893765-38893775 chr19:38893763-38893772 chr19:38893763-38893776 chr19:38893947-38893960 chr19:38893763-38893776 chr19:38893760-38893778 chr19:38893904-38893917 chr19:38893761-38893777 chr19:38893569-38893579
29	TCF12	chr19:38893463-38894515	ECC-1	luminal epithelium:	n/a	n/a
30	JUND	chr19:38893494-38894524	A549	lung:	n/a	chr19:38894152-38894161 chr19:38893652-38893661
31	SIN3AK20	chr19:38893191-38894231	A549	lung:	n/a	n/a
32	POLR2A	chr19:38893306-38894423	GM12878	blood:	n/a	n/a
33	MAX	chr19:38893332-38894300	NB4	blood:	n/a	chr19:38894146-38894156 chr19:38893956-38893966 chr19:38893946-38893956 chr19:38894160-38894169
34	MAZ	chr19:38893309-38894215	HepG2	liver:	n/a	chr19:38894146-38894156 chr19:38893956-38893966 chr19:38893946-38893956 chr19:38894160-38894169
35	POLR2A	chr19:38893397-38894225	Gliobla	brain:	n/a	n/a
36	TCF12	chr19:38893028-38894554	A549	lung:	n/a	n/a
37	UBTF	chr19:38893409-38894477	K562	blood:	n/a	n/a
38	ZNF143	chr19:38893396-38893973	K562	blood:	n/a	n/a
39	RCOR1	chr19:38893227-38894434	K562	blood:	n/a	n/a
40	POLR2A	chr19:38893652-38893943	U87	brain:	n/a	n/a
41	SIN3A	chr19:38893412-38894347	GM12878	blood:	n/a	chr19:38893565-38893574
42	POLR2A	chr19:38893439-38894419	A549	lung:	n/a	n/a
43	MTA3	chr19:38893591-38894311	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:38893336-38894473	GM12878	blood:	n/a	n/a
45	TAF1	chr19:38893617-38894331	HepG2	liver:	n/a	n/a
46	RAD21	chr19:38893390-38893981	HepG2	liver:	n/a	chr19:38893904-38893914 chr19:38893766-38893776 chr19:38893902-38893914 chr19:38893761-38893780
47	ZBTB7A	chr19:38893501-38894458	ECC-1	luminal epithelium:	n/a	chr19:38893768-38893777
48	PAX5	chr19:38893585-38893991	GM12878	blood:	n/a	n/a
49	ELF1	chr19:38893452-38894074	MCF-7	breast:	n/a	n/a
50	GABPA	chr19:38893560-38894075	A549	lung:	n/a	chr19:38893945-38893954 chr19:38893728-38893737

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38893916-38893966	HMEC	breast:	n/a
2	chr19:38893916-38893966	RPTEC	kidney:	n/a
3	chr19:38893916-38893966	MCF10A-Er-Src	breast:	n/a
4	chr19:38893916-38893966	AG04449	skin:	fetal
5	chr19:38893916-38893966	AG09319	gingival:	n/a
6	chr19:38893916-38893966	HCT-116	colon:	n/a
7	chr19:38893916-38893966	HPAEpiC	pulmonary alveolar:	n/a
8	chr19:38893916-38893966	NB4	blood:	n/a
9	chr19:38893916-38893966	GM06990	blood:	n/a
10	chr19:38893916-38893966	PFSK-1	brain:	n/a
11	chr19:38893916-38893966	GM12892	blood:	n/a
12	chr19:38893916-38893966	AoSMC	blood vessel:	n/a
13	chr19:38893916-38893966	A549	lung:	n/a
14	chr19:38893916-38893966	Hepatocyte	liver:	n/a
15	chr19:38893916-38893966	T-47D	breast:	n/a
16	chr19:38893916-38893966	IMR90	lung:	fetal
17	chr19:38893916-38893966	ProgFib	skin:	n/a
18	chr19:38893916-38893966	HEEpiC	esophagus:	n/a
19	chr19:38893916-38893966	HL-60	blood:	n/a
20	chr19:38893916-38893966	SAEC	small airway:	n/a
21	chr19:38893916-38893966	ECC-1	luminal epithelium:	n/a
22	chr19:38893916-38893966	Hela-S3	cervix:	n/a
23	chr19:38893916-38893966	HUVEC	blood vessel:	n/a
24	chr19:38893916-38893966	NT2-D1	testis:	n/a
25	chr19:38893916-38893966	SK-N-MC	brain:	n/a
26	chr19:38893916-38893966	K562	blood:	n/a
27	chr19:38893916-38893966	HepG2	liver:	n/a
28	chr19:38893916-38893966	HRE	kidney:	n/a
29	chr19:38893916-38893966	PrEC	prostate:	n/a
30	chr19:38893916-38893966	AG04450	lung:	fetal
31	chr19:38893916-38893966	BE2_C	brain:	n/a
32	chr19:38893916-38893966	PANC-1	pancreas:	n/a
33	chr19:38893916-38893966	MCF-7	breast:	n/a
34	chr19:38893916-38893966	HAEpiC	amniotic membrane:	n/a
35	chr19:38893916-38893966	GM19239	blood:	n/a
36	chr19:38893916-38893966	NHDF-neo	bronchial:	n/a
37	chr19:38893916-38893966	H1-hESC	embryonic stem cell:	embryo
38	chr19:38893916-38893966	HRCEpiC	kidney:	n/a
39	chr19:38893916-38893966	GM12891	blood:	n/a
40	chr19:38893916-38893966	Caco-2	colon:	n/a
41	chr19:38893916-38893966	SK-N-SH_RA	brain:	n/a
42	chr19:38893916-38893966	CMK	blood:	n/a
43	chr19:38893916-38893966	ovcar-3	ovarian:	n/a
44	chr19:38893916-38893966	BJ	skin:	n/a
45	chr19:38893916-38893966	HRPEpiC	eye:	n/a
46	chr19:38893916-38893966	SK-N-SH	brain:	n/a
47	chr19:38893916-38893966	AG09309	skin:	n/a
48	chr19:38893916-38893966	HCF	heart:	n/a
49	chr19:38893916-38893966	SKMC	muscle:	n/a
50	chr19:38893916-38893966	AG10803	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38878247..38879210-chr19:38893527..38894426,2	K562	blood:
2	chr19:38892832..38895683-chr19:38905614..38908476,2	K562	blood:
3	chr19:38892751..38895518-chr19:38905731..38908056,2	MCF-7	breast:
4	chr19:38864731..38867116-chr19:38892888..38894994,2	MCF-7	breast:
5	chr19:38864536..38866994-chr19:38891927..38895682,4	MCF-7	breast:
6	chr19:38825542..38827860-chr19:38892803..38895034,2	K562	blood:
7	chr19:38886501..38890187-chr19:38891290..38894154,6	MCF-7	breast:
8	chr19:38893264..38895978-chr19:39340017..39342861,2	MCF-7	breast:
9	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
10	chr19:38891109..38897587-chr19:38900077..38906045,7	MCF-7	breast:
11	chr19:38892840..38895111-chr19:38906916..38908853,2	MCF-7	breast:
12	chr19:38810024..38812525-chr19:38892478..38895075,3	MCF-7	breast:
13	chr19:38891977..38893968-chr19:38915428..38917384,2	K562	blood:
14	chr19:38878160..38880019-chr19:38892423..38895031,2	MCF-7	breast:

Variant related genes	Relation type
FAM98C	TF binding region
FAM98C	CpG island
ENSG00000099341	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000099337	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000171777	Chromatin interaction
ENSG00000267473	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1077994	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12608722	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12609258	0.83[AMR][1000 genomes]
rs12609878	0.83[EUR][1000 genomes]
rs12610650	0.91[ASN][1000 genomes]
rs2074982	0.82[ASN][1000 genomes]
rs3745957	0.85[ASN][1000 genomes]
rs3745959	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959303	0.82[ASN][1000 genomes]
rs56854837	0.82[ASN][1000 genomes]
rs57146784	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58462889	0.85[ASN][1000 genomes]
rs59491640	0.81[AFR][1000 genomes]
rs61162240	0.83[EUR][1000 genomes]
rs6508790	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38893000-38894400	Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:38893200-38894000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr19:38893200-38894200	Active TSS	HMEC	breast
4	chr19:38893200-38894400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:38893200-38894400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr19:38893200-38894400	Active TSS	Fetal Lung	lung
7	chr19:38893200-38894600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:38893200-38894600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr19:38893200-38894600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:38893200-38894600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:38893200-38894600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:38893200-38894600	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:38893200-38894600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:38893200-38894600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:38893200-38894600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:38893200-38894600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:38893200-38894600	Active TSS	Brain Cingulate Gyrus	brain
18	chr19:38893200-38894600	Active TSS	Brain Substantia Nigra	brain
19	chr19:38893200-38894600	Active TSS	Colon Smooth Muscle	Colon
20	chr19:38893200-38894600	Active TSS	Esophagus	oesophagus
21	chr19:38893200-38894600	Active TSS	Fetal Kidney	kidney
22	chr19:38893200-38894600	Active TSS	Left Ventricle	heart
23	chr19:38893200-38894600	Active TSS	Lung	lung
24	chr19:38893200-38894600	Active TSS	Ovary	ovary
25	chr19:38893200-38894600	Active TSS	Psoas Muscle	Psoas
26	chr19:38893200-38894600	Active TSS	Right Atrium	heart
27	chr19:38893200-38894600	Active TSS	Right Ventricle	heart
28	chr19:38893200-38894600	Active TSS	HSMM	muscle
29	chr19:38893200-38894600	Active TSS	HSMMtube	muscle
30	chr19:38893200-38894600	Active TSS	NHDF-Ad	bronchial
31	chr19:38893200-38894600	Active TSS	NHLF	lung
32	chr19:38893200-38894800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38893200-38894800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:38893200-38894800	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr19:38893200-38894800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr19:38893200-38894800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:38893200-38894800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:38893200-38894800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:38893200-38894800	Active TSS	Primary T cells from cord blood	blood
40	chr19:38893200-38894800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:38893200-38894800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:38893200-38894800	Active TSS	Muscle Satellite Cultured Cells	--
43	chr19:38893200-38894800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:38893200-38894800	Active TSS	Brain Angular Gyrus	brain
45	chr19:38893200-38894800	Active TSS	Brain Hippocampus Middle	brain
46	chr19:38893200-38894800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:38893200-38894800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr19:38893200-38894800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr19:38893200-38894800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr19:38893200-38894800	Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links