Variant report

Variant	rs2318459
Chromosome Location	chr19:39326754-39326755
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:110)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:110 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39325351-39335703	K562	blood:	n/a	n/a
2	POLR2A	chr19:39326009-39326979	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:39325898-39327104	HCT-116	colon:	n/a	n/a
4	POLR2A	chr19:39325903-39327016	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:39325224-39327147	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:39326577-39326840	HUVEC	blood vessel:	n/a	n/a
7	ETS1	chr19:39325938-39327074	A549	lung:	n/a	n/a
8	POLR2A	chr19:39326543-39326972	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr19:39325327-39327188	K562	blood:	n/a	n/a
10	POLR2A	chr19:39325991-39326936	GM12878	blood:	n/a	n/a
11	CTCF	chr19:39326700-39326850	HEK293	kidney:	n/a	n/a
12	BCL3	chr19:39325179-39327051	A549	lung:	n/a	n/a
13	POLR2A	chr19:39325914-39326950	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr19:39325852-39326941	A549	lung:	n/a	n/a
15	POLR2A	chr19:39325875-39326938	HUVEC	blood vessel:	n/a	n/a
16	PML	chr19:39325902-39327130	K562	blood:	n/a	n/a
17	POLR2A	chr19:39325825-39327117	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
19	SIN3AK20	chr19:39325948-39327022	A549	lung:	n/a	n/a
20	SP1	chr19:39325835-39326928	A549	lung:	n/a	n/a
21	POLR2A	chr19:39325896-39330910	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:39325927-39327037	HL-60	blood:	n/a	n/a
23	POLR2A	chr19:39325377-39335667	A549	lung:	n/a	n/a
24	TCF12	chr19:39325292-39327031	A549	lung:	n/a	n/a
25	PBX3	chr19:39325905-39326994	A549	lung:	n/a	n/a
26	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
27	ATF2	chr19:39326167-39327035	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:39325298-39335742	GM12892	blood:	n/a	n/a
29	PML	chr19:39326546-39327010	K562	blood:	n/a	n/a
30	POLR2A	chr19:39326051-39327104	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr19:39326416-39326932	GM15510	blood:	n/a	n/a
33	POLR2A	chr19:39325268-39330971	PFSK-1	brain:	n/a	n/a
34	MAX	chr19:39325841-39327002	A549	lung:	n/a	n/a
35	POLR2A	chr19:39325983-39327036	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr19:39325690-39327058	SK-N-SH	brain:	n/a	n/a
37	SIN3AK20	chr19:39325169-39327064	PANC-1	pancreas:	n/a	n/a
38	FOSL2	chr19:39325907-39327129	A549	lung:	n/a	chr19:39326312-39326324
39	POLR2A	chr19:39326034-39327023	HepG2	liver:	n/a	n/a
40	POLR2A	chr19:39325282-39327124	U87	brain:	n/a	n/a
41	POLR2A	chr19:39325772-39327036	HL-60	blood:	n/a	n/a
42	SP1	chr19:39325882-39326838	A549	lung:	n/a	n/a
43	NFATC1	chr19:39325816-39326988	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:39326517-39327024	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:39325282-39327139	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:39325908-39326899	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr19:39325170-39335506	H1-hESC	embryonic stem cell:	n/a	n/a
48	GATA3	chr19:39325171-39326780	A549	lung:	n/a	n/a
49	POLR2A	chr19:39325861-39327053	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:39326034-39326902	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39221972..39229243-chr19:39319630..39326763,11	K562	blood:
2	chr19:39326299..39328911-chr19:39388226..39390640,3	K562	blood:
3	chr19:39326299..39328674-chr19:39389140..39390810,2	K562	blood:
4	chr19:39326367..39329872-chr19:39419342..39422625,3	MCF-7	breast:
5	chr19:39324931..39327493-chr19:39358939..39361060,2	MCF-7	breast:
6	chr19:39315714..39318484-chr19:39324884..39327703,2	K562	blood:
7	chr19:39218553..39228703-chr19:39324875..39331730,17	MCF-7	breast:
8	chr19:39325997..39327543-chr19:39409428..39411815,2	K562	blood:
9	chr19:39325391..39328182-chr19:39375242..39377449,2	K562	blood:

No data

Variant related genes	Relation type
ECH1	TF binding region
ENSG00000269050	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000068903	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1103435	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2113123	0.99[EUR][1000 genomes]
rs2113124	0.96[EUR][1000 genomes]
rs2278009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278011	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278012	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35812434	0.81[EUR][1000 genomes]
rs6508822	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67859595	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7246134	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255774	0.98[ASN][1000 genomes]
rs8104416	0.95[EUR][1000 genomes]
rs8104420	0.98[EUR][1000 genomes]
rs862455	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862459	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862464	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9789283	0.89[EUR][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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv961291	chr19:39324891-39329561	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2318459	ECH1	Cis_1M	lymphoblastoid	RTeQTL
rs2318459	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL
rs2318459	HNRNPL	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39322400-39331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39322600-39327400	Weak transcription	Small Intestine	intestine
3	chr19:39323000-39327200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:39323000-39334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:39323200-39327000	Weak transcription	NHDF-Ad	bronchial
6	chr19:39323200-39327400	Weak transcription	Aorta	Aorta
7	chr19:39323400-39326800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:39323400-39327600	Weak transcription	Right Atrium	heart
9	chr19:39324600-39338000	Strong transcription	Fetal Brain Female	brain
10	chr19:39325000-39327600	Strong transcription	Fetal Intestine Small	intestine
11	chr19:39325000-39334000	Strong transcription	Fetal Stomach	stomach
12	chr19:39325200-39331600	Strong transcription	Primary T cells from cord blood	blood
13	chr19:39325400-39327000	Genic enhancers	Fetal Muscle Leg	muscle
14	chr19:39325400-39327800	Strong transcription	Lung	lung
15	chr19:39325400-39328600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:39325400-39329200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:39325400-39329800	Genic enhancers	Fetal Lung	lung
18	chr19:39325400-39331200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:39325400-39331600	Strong transcription	Fetal Thymus	thymus
20	chr19:39325400-39332000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:39325400-39332200	Strong transcription	Thymus	Thymus
22	chr19:39325400-39336800	Strong transcription	Brain Substantia Nigra	brain
23	chr19:39325400-39337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:39325400-39337800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr19:39325400-39338000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr19:39325400-39338200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:39325400-39338200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:39325600-39327600	Genic enhancers	Osteobl	bone
29	chr19:39325600-39329400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:39325600-39333600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:39325600-39338000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:39325800-39328400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr19:39325800-39330800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:39326000-39326800	Genic enhancers	Colon Smooth Muscle	Colon
35	chr19:39326000-39326800	Strong transcription	Fetal Intestine Large	intestine
36	chr19:39326000-39326800	Genic enhancers	NH-A	brain
37	chr19:39326000-39327000	Transcr. at gene 5' and 3'	A549	lung
38	chr19:39326000-39327400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:39326000-39327400	Genic enhancers	Liver	Liver
40	chr19:39326000-39327600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:39326000-39327600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:39326000-39328000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr19:39326000-39328200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:39326000-39328200	Genic enhancers	Stomach Smooth Muscle	stomach
45	chr19:39326000-39328400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:39326000-39328600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:39326000-39328600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr19:39326000-39329200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:39326000-39331000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr19:39326000-39331200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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