Variant report

Variant	rs3745213
Chromosome Location	chr19:41248009-41248010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr19:41247545-41248169	NB4	blood:	n/a	chr19:41247602-41247612
2	POLR2A	chr19:41247394-41248241	H1-hESC	embryonic stem cell:	n/a	n/a
3	BCL3	chr19:41247366-41248172	A549	lung:	n/a	n/a
4	CTCF	chr19:41248000-41248188	K562	blood:	n/a	n/a
5	POLR2A	chr19:41247302-41248869	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr19:41248000-41248150	WERI-Rb-1	eye:	n/a	n/a
7	POLR2A	chr19:41247463-41249035	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr19:41247951-41248251	K562	blood:	n/a	n/a
9	POLR2A	chr19:41247331-41248953	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr19:41245709-41249072	HepG2	liver:	n/a	n/a
11	CTCF	chr19:41248000-41248150	HEK293	kidney:	n/a	n/a
12	POLR2A	chr19:41247207-41248325	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:41247319-41249007	K562	blood:	n/a	n/a
14	POLR2A	chr19:41247403-41248751	MCF-7	breast:	n/a	n/a
15	POLR2A	chr19:41247341-41248527	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr19:41247425-41248078	HepG2	liver:	n/a	n/a
17	MYC	chr19:41247498-41248082	K562	blood:	n/a	chr19:41247602-41247612
18	POLR2A	chr19:41247868-41248259	U87	brain:	n/a	n/a
19	POLR2A	chr19:41247451-41248108	Hela-S3	cervix:	n/a	n/a
20	HMGN3	chr19:41247933-41248514	K562	blood:	n/a	n/a
21	CTCF	chr19:41247980-41248130	K562	blood:	n/a	n/a
22	POLR2A	chr19:41247424-41248688	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:41247390-41248954	K562	blood:	n/a	n/a
24	POLR2A	chr19:41247510-41248894	A549	lung:	n/a	n/a
25	POLR2A	chr19:41247405-41249010	HepG2	liver:	n/a	n/a
26	CTCF	chr19:41247980-41248130	SAEC	small airway:	n/a	n/a
27	POLR2A	chr19:41247711-41248553	U87	brain:	n/a	n/a
28	POLR2A	chr19:41247950-41248307	A549	lung:	n/a	n/a
29	RAD21	chr19:41247972-41248187	K562	blood:	n/a	n/a
30	CTCF	chr19:41247960-41248110	HMEC	breast:	n/a	n/a
31	RAD21	chr19:41247972-41248136	SK-N-SH_RA	brain:	n/a	n/a
32	POLR2A	chr19:41247801-41248051	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr19:41247964-41248298	K562	blood:	n/a	n/a
34	POLR2A	chr19:41247872-41248069	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:41247308-41248028	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr19:41245113-41248614	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41246510..41248162-chr19:41281990..41283890,2	K562	blood:
2	chr19:41246355..41251647-chr19:41252986..41257062,8	MCF-7	breast:

No data

Variant related genes	Relation type
C19orf54	TF binding region
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000261857	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10401344	0.92[JPT][hapmap]
rs10403040	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs10405596	0.85[JPT][hapmap]
rs10426415	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11083567	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs11083568	0.85[JPT][hapmap]
rs11881124	0.84[JPT][hapmap]
rs17713068	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2233152	0.85[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap]
rs2287691	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2287692	0.88[CHD][hapmap];0.93[JPT][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs2288450	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28493229	0.94[EUR][1000 genomes];1.00[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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3745213	FOXA3	cis	parietal	SCAN
rs3745213	CIC	cis	parietal	SCAN
rs3745213	ZNF230	cis	cerebellum	SCAN
rs3745213	HSD17B14	cis	cerebellum	SCAN
rs3745213	LIN7B	cis	parietal	SCAN
rs3745213	IGFL1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
3	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:41228600-41251000	Strong transcription	Fetal Brain Female	brain
5	chr19:41229400-41249000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:41229800-41248600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:41229800-41248600	Strong transcription	Dnd41	blood
8	chr19:41229800-41249200	Strong transcription	Thymus	Thymus
9	chr19:41229800-41250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:41233600-41248400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:41233600-41249200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr19:41234800-41248400	Strong transcription	Gastric	stomach
13	chr19:41237000-41255400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:41237600-41255200	Weak transcription	Fetal Brain Male	brain
15	chr19:41239400-41250000	Strong transcription	Spleen	Spleen
16	chr19:41240200-41255600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:41241600-41251000	Weak transcription	NH-A	brain
18	chr19:41241800-41248800	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr19:41242000-41250600	Strong transcription	Fetal Intestine Small	intestine
20	chr19:41242000-41253800	Weak transcription	GM12878-XiMat	blood
21	chr19:41242200-41255600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr19:41242400-41251000	Weak transcription	Hela-S3	cervix
23	chr19:41242600-41250200	Strong transcription	Fetal Intestine Large	intestine
24	chr19:41243200-41251200	Weak transcription	Fetal Kidney	kidney
25	chr19:41243400-41248400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:41243400-41254400	Weak transcription	Psoas Muscle	Psoas
27	chr19:41243600-41255600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr19:41243800-41249400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:41243800-41255400	Weak transcription	HSMM	muscle
30	chr19:41244000-41250800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:41245000-41250200	Genic enhancers	Placenta	Placenta
32	chr19:41245000-41251000	Weak transcription	HUVEC	blood vessel
33	chr19:41245000-41254600	Weak transcription	Stomach Mucosa	stomach
34	chr19:41245000-41255400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:41245200-41248200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
36	chr19:41245200-41254400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:41245600-41251000	Weak transcription	Osteobl	bone
38	chr19:41245600-41251200	Weak transcription	HSMMtube	muscle
39	chr19:41245600-41255600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr19:41245800-41249600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:41245800-41249800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr19:41245800-41255400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:41246000-41250000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:41246000-41255600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr19:41246200-41251000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:41246200-41254400	Weak transcription	Brain Substantia Nigra	brain
47	chr19:41246200-41255400	Weak transcription	Brain Angular Gyrus	brain
48	chr19:41246200-41255400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:41246200-41255400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:41246200-41255600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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