Variant report

Variant	rs3848619
Chromosome Location	chr19:55677523-55677524
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	SMARCC2	chr19:55677250-55677719	Hela-S3	cervix:	n/a	chr19:55677445-55677454
2	CREB1	chr19:55677212-55678393	A549	lung:	n/a	n/a
3	ELF1	chr19:55677276-55677912	A549	lung:	n/a	n/a
4	CTCF	chr19:55677480-55677630	GM12872	blood:	n/a	chr19:55677561-55677574
5	MAX	chr19:55677400-55677689	K562	blood:	n/a	n/a
6	MYBL2	chr19:55677365-55677800	HepG2	liver:	n/a	n/a
7	CTCF	chr19:55677225-55678029	MCF-7	breast:	n/a	chr19:55677561-55677574
8	SIN3AK20	chr19:55677388-55677790	K562	blood:	n/a	n/a
9	CTCF	chr19:55677218-55678000	A549	lung:	n/a	chr19:55677561-55677574
10	MXI1	chr19:55677281-55677649	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr19:55677480-55677630	GM12874	blood:	n/a	chr19:55677561-55677574
12	YY1	chr19:55677396-55677721	HCT-116	colon:	n/a	n/a
13	GTF2F1	chr19:55677250-55677731	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr19:55677432-55677688	K562	blood:	n/a	n/a
15	CTCF	chr19:55677380-55677530	HAc	cerebellar:	n/a	n/a
16	ETS1	chr19:55677116-55677875	K562	blood:	n/a	chr19:55677444-55677457 chr19:55677443-55677456
17	NR2F2	chr19:55677218-55678548	K562	blood:	n/a	n/a
18	GABPA	chr19:55677142-55678218	K562	blood:	n/a	n/a
19	CTCF	chr19:55677494-55677677	GM10248	blood:	n/a	chr19:55677561-55677574
20	CTCF	chr19:55677381-55677930	A549	lung:	n/a	chr19:55677561-55677574
21	RAD21	chr19:55677392-55677672	SK-N-SH_RA	brain:	n/a	n/a
22	CREB1	chr19:55677273-55678376	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr19:55677480-55677630	SK-N-SH_RA	brain:	n/a	chr19:55677561-55677574
24	RCOR1	chr19:55677348-55679357	Hela-S3	cervix:	n/a	n/a
25	GABPA	chr19:55677328-55677718	SK-N-SH	brain:	n/a	n/a
26	ZMIZ1	chr19:55677402-55677697	K562	blood:	n/a	n/a
27	CTCF	chr19:55677460-55677610	GM12865	blood:	n/a	chr19:55677561-55677574
28	MXI1	chr19:55677412-55678666	Hela-S3	cervix:	n/a	chr19:55678148-55678163 chr19:55678146-55678161
29	HCFC1	chr19:55677117-55678511	K562	blood:	n/a	n/a
30	CTCF	chr19:55677500-55677650	GM12865	blood:	n/a	chr19:55677561-55677574
31	CTCF	chr19:55677440-55677590	HFF	foreskin:	n/a	chr19:55677561-55677574
32	USF2	chr19:55677391-55678669	Hela-S3	cervix:	n/a	chr19:55677560-55677576
33	EP300	chr19:55677401-55677619	K562	blood:	n/a	chr19:55677546-55677562
34	CTCF	chr19:55677397-55677746	MCF-7	breast:	n/a	chr19:55677561-55677574
35	CTCF	chr19:55677321-55677936	NHEK	skin:	n/a	chr19:55677561-55677574
36	CTCF	chr19:55677234-55678002	K562	blood:	n/a	chr19:55677561-55677574
37	CHD2	chr19:55677306-55678568	Hela-S3	cervix:	n/a	chr19:55678401-55678411
38	CTCF	chr19:55677480-55677630	AG04450	lung:	n/a	chr19:55677561-55677574
39	CTCF	chr19:55677301-55677926	MCF-7	breast:	n/a	chr19:55677561-55677574
40	SIX5	chr19:55677276-55677579	GM12878	blood:	n/a	chr19:55677447-55677456 chr19:55677445-55677454
41	CTCF	chr19:55677460-55677610	HMF	breast:	n/a	chr19:55677561-55677574
42	KAP1	chr19:55677334-55677772	HEK293	kidney:	n/a	n/a
43	ELK1	chr19:55677402-55678648	Hela-S3	cervix:	n/a	n/a
44	CCNT2	chr19:55677243-55678286	K562	blood:	n/a	n/a
45	CTCF	chr19:55677460-55677610	BJ	skin:	n/a	chr19:55677561-55677574
46	CTCF	chr19:55677480-55677630	HCFaa	heart:	n/a	chr19:55677561-55677574
47	ELF1	chr19:55677437-55677658	K562	blood:	n/a	n/a
48	TCF7L2	chr19:55677370-55678721	HCT-116	colon:	n/a	n/a
49	THAP1	chr19:55677425-55677822	K562	blood:	n/a	n/a
50	MAX	chr19:55677266-55678748	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55676623..55678727-chr19:55917591..55919258,2	MCF-7	breast:
2	chr19:55669094..55672573-chr19:55676633..55678240,3	K562	blood:
3	chr19:55677411..55679148-chr19:55895317..55896952,2	MCF-7	breast:
4	chr19:55676191..55679387-chr19:55917452..55919839,3	K562	blood:
5	chr19:55676374..55679520-chr19:55726674..55730754,4	K562	blood:
6	chr19:55592134..55595044-chr19:55674815..55678963,4	K562	blood:
7	chr19:55676207..55678218-chr19:55894877..55897476,2	MCF-7	breast:
8	chr19:55666873..55668722-chr19:55676430..55678695,2	K562	blood:
9	chr19:55672196..55674741-chr19:55676544..55679173,3	K562	blood:
10	chr19:55677235..55679036-chr19:55897209..55898733,2	K562	blood:
11	chr19:55675848..55678136-chr19:55894504..55899983,4	K562	blood:
12	chr19:55590129..55594149-chr19:55677127..55678963,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55677187-55678229	NONHSAT067999

Variant related genes	Relation type
ENSG00000239137	TF binding region
DNAAF3	TF binding region
ENSG00000108107	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000267577	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267649	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10422172	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671293	0.91[ASN][1000 genomes]
rs28377509	0.91[ASN][1000 genomes]
rs3729836	0.91[ASN][1000 genomes]
rs3729838	0.91[ASN][1000 genomes]
rs3786866	0.87[ASN][1000 genomes]
rs6509933	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3848619	DNAAF3	cis	Thyroid	GTEx
rs3848619	CTD-2587H24.5	cis	Thyroid	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55671600-55677600	Weak transcription	Right Atrium	heart
2	chr19:55671800-55677600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:55677000-55677600	Flanking Active TSS	Hela-S3	cervix
4	chr19:55677000-55677800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:55677000-55678000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:55677000-55678400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:55677200-55677600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:55677200-55677600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:55677200-55677600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:55677200-55677600	Enhancers	Esophagus	oesophagus
11	chr19:55677200-55677600	Bivalent Enhancer	Fetal Intestine Small	intestine
12	chr19:55677200-55677600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr19:55677200-55677600	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr19:55677200-55677600	Bivalent Enhancer	Placenta	Placenta
15	chr19:55677200-55677600	Enhancers	Gastric	stomach
16	chr19:55677200-55677600	Enhancers	Left Ventricle	heart
17	chr19:55677200-55677600	Enhancers	Pancreas	Pancrea
18	chr19:55677200-55677600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr19:55677200-55677600	Enhancers	Psoas Muscle	Psoas
20	chr19:55677200-55677800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
21	chr19:55677200-55677800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:55677200-55678000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:55677200-55678000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
24	chr19:55677200-55678400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:55677200-55678400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:55677200-55678400	Active TSS	Brain Anterior Caudate	brain
27	chr19:55677200-55678400	Bivalent/Poised TSS	Colonic Mucosa	Colon
28	chr19:55677200-55678400	Active TSS	HSMM	muscle
29	chr19:55677200-55678600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:55677200-55678600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr19:55677200-55678600	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr19:55677200-55678600	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr19:55677200-55678600	Active TSS	Muscle Satellite Cultured Cells	--
34	chr19:55677200-55678800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:55677200-55678800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
36	chr19:55677200-55679000	Enhancers	Spleen	Spleen
37	chr19:55677200-55679200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr19:55677400-55677600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:55677400-55677600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:55677400-55677600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:55677400-55677600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr19:55677400-55677600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:55677400-55677600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:55677400-55677600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:55677400-55677600	Enhancers	Liver	Liver
46	chr19:55677400-55677600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
47	chr19:55677400-55677600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
48	chr19:55677400-55677600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
49	chr19:55677400-55677600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
50	chr19:55677400-55677600	Bivalent Enhancer	Fetal Stomach	stomach

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