Variant report

Variant	rs2278012
Chromosome Location	chr19:39334830-39334831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

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	chr19:39334430-39335257	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:39332763-39335421	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:39334743-39335135	A549	lung:	n/a	n/a
6	POLR2A	chr19:39334371-39334964	MCF-7	breast:	n/a	n/a
7	POLR2A	chr19:39334603-39335140	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr19:39334788-39335325	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:39332880-39335316	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:39332949-39335437	HL-60	blood:	n/a	n/a
12	POLR2A	chr19:39325377-39335667	A549	lung:	n/a	n/a
13	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:39327254-39335682	GM12891	blood:	n/a	n/a
15	POLR2A	chr19:39334552-39334861	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:39325298-39335742	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:39330872-39335592	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
19	HEY1	chr19:39332846-39335679	K562	blood:	n/a	n/a
20	POLR2A	chr19:39331212-39335417	GM12891	blood:	n/a	n/a
21	POLR2A	chr19:39327162-39334961	HCT-116	colon:	n/a	n/a
22	POLR2A	chr19:39333075-39335322	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr19:39333485-39335276	U87	brain:	n/a	n/a
24	POLR2A	chr19:39327320-39335679	K562	blood:	n/a	n/a
25	POLR2A	chr19:39325170-39335506	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:39332871-39335139	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:39334335-39335276	U87	brain:	n/a	n/a
28	POLR2A	chr19:39333060-39335258	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:39334405-39335524	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr19:39334428-39335289	K562	blood:	n/a	n/a
31	POLR2A	chr19:39334696-39335052	SK-N-SH	brain:	n/a	n/a
32	JUND	chr19:39334392-39334903	A549	lung:	n/a	n/a
33	POLR2A	chr19:39330876-39335627	GM12892	blood:	n/a	n/a
34	POLR2A	chr19:39332413-39335181	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr19:39334266-39335380	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:39332757-39335761	HepG2	liver:	n/a	n/a
37	POLR2A	chr19:39332137-39335714	H1-hESC	embryonic stem cell:	n/a	n/a
38	HEY1	chr19:39334744-39335253	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:39331194-39335342	HepG2	liver:	n/a	n/a
40	POLR2A	chr19:39334788-39335166	A549	lung:	n/a	n/a
41	POLR2A	chr19:39334758-39335174	A549	lung:	n/a	n/a
42	POLR2A	chr19:39332432-39335734	K562	blood:	n/a	n/a
43	POLR2A	chr19:39334624-39335589	K562	blood:	n/a	n/a
44	POLR2A	chr19:39334585-39335661	H1-hESC	embryonic stem cell:	n/a	n/a
45	HEY1	chr19:39334772-39335423	HepG2	liver:	n/a	n/a
46	POLR2A	chr19:39325950-39335545	HepG2	liver:	n/a	n/a
47	POLR2A	chr19:39334155-39334919	K562	blood:	n/a	n/a
48	POLR2A	chr19:39325704-39335757	GM12892	blood:	n/a	n/a
49	POLR2A	chr19:39332760-39335673	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr19:39331012-39342704	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39332878..39335584-chr19:39408217..39410062,2	MCF-7	breast:
2	chr19:39233896..39236050-chr19:39333989..39336048,2	K562	blood:
3	chr19:39221339..39223796-chr19:39333308..39334963,2	MCF-7	breast:
4	chr19:39306612..39310061-chr19:39334754..39339038,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268083	TF binding region
HNRNPL	TF binding region
ENSG00000104835	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1001413	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs1103435	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668766	0.80[CEU][hapmap]
rs2113123	0.95[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2113124	0.96[EUR][1000 genomes]
rs2278009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318459	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496951	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap]
rs35812434	0.81[EUR][1000 genomes]
rs6508822	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67859595	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7246134	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255774	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8100220	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs8104416	0.95[EUR][1000 genomes]
rs8104420	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs862455	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862459	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862464	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9789283	0.89[EUR][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2278012	HNRNPL	N/A	lymphoblastoid	RTeQTL
rs2278012	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL
rs2278012	ECH1	Cis_1M	lymphoblastoid	RTeQTL
rs2278012	HNRNPL	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39324600-39338000	Strong transcription	Fetal Brain Female	brain
2	chr19:39325400-39336800	Strong transcription	Brain Substantia Nigra	brain
3	chr19:39325400-39337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:39325400-39337800	Strong transcription	Brain Cingulate Gyrus	brain
5	chr19:39325400-39338000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:39325400-39338200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr19:39325400-39338200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr19:39325600-39338000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:39326000-39336200	Strong transcription	Brain Hippocampus Middle	brain
10	chr19:39326000-39336600	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr19:39326000-39337000	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr19:39326000-39337800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:39326000-39338000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:39326000-39338000	Strong transcription	Brain Anterior Caudate	brain
15	chr19:39326000-39338000	Strong transcription	HSMM	muscle
16	chr19:39326000-39338200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:39326000-39338200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:39326000-39338200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:39326000-39338200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr19:39326000-39338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr19:39326000-39338400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:39326000-39338400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr19:39326000-39338600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr19:39326200-39337000	Strong transcription	Primary hematopoietic stem cells	blood
25	chr19:39326200-39337600	Strong transcription	Ovary	ovary
26	chr19:39326200-39337800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:39326200-39337800	Strong transcription	Right Ventricle	heart
28	chr19:39326200-39337800	Strong transcription	HUVEC	blood vessel
29	chr19:39326200-39337800	Strong transcription	K562	blood
30	chr19:39326200-39338000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:39326200-39338000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr19:39326200-39338200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr19:39326200-39338400	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr19:39326200-39338400	Strong transcription	Fetal Kidney	kidney
35	chr19:39326200-39338800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:39326400-39335000	Genic enhancers	Pancreas	Pancrea
37	chr19:39326400-39335200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr19:39326400-39338200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:39326400-39338400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr19:39326600-39336800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr19:39326600-39337800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:39326600-39338200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:39326800-39336200	Strong transcription	Colon Smooth Muscle	Colon
44	chr19:39326800-39337800	Strong transcription	NH-A	brain
45	chr19:39326800-39338000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:39326800-39338000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:39327000-39337000	Strong transcription	HSMMtube	muscle
48	chr19:39327000-39337800	Strong transcription	Rectal Smooth Muscle	rectum
49	chr19:39327000-39338400	Strong transcription	NHDF-Ad	bronchial
50	chr19:39327600-39337800	Genic enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links