Variant report

Variant	rs3088389
Chromosome Location	chr1:227919190-227919191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227910908-227920562	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:227915589-227919836	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:227914982-227921463	K562	blood:	n/a	n/a
4	POLR2A	chr1:227916272-227919690	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:227910941-227920625	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:227916673-227919956	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:227915709-227919959	GM18951	blood:	n/a	n/a
8	POLR2A	chr1:227918934-227920392	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr1:227915712-227919917	K562	blood:	n/a	n/a
10	POLR2A	chr1:227915746-227919787	GM19099	blood:	n/a	n/a
11	POLR2A	chr1:227916413-227919627	K562	blood:	n/a	n/a
12	POLR2A	chr1:227915592-227919533	MCF-7	breast:	n/a	n/a
13	POLR2A	chr1:227914179-227919823	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:227915658-227920836	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:227914462-227920881	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:227916824-227919789	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:227917854-227919491	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:227914027-227920701	GM12891	blood:	n/a	n/a
19	BHLHE40	chr1:227918111-227919312	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:227916211-227920587	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr1:227916271-227919957	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr1:227916302-227920154	PBDE	blood:	n/a	n/a
23	POLR2A	chr1:227915700-227921841	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:227914208-227920934	K562	blood:	n/a	n/a
25	POLR2A	chr1:227915624-227920666	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:227916775-227920355	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr1:227917419-227919226	HCT-116	colon:	n/a	n/a
28	POLR2A	chr1:227916242-227920809	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:227915660-227921896	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:227915742-227920103	GM19193	blood:	n/a	n/a
31	POLR2A	chr1:227918931-227919983	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:227919156-227919487	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:227915827-227919659	GM15510	blood:	n/a	n/a
34	POLR2A	chr1:227915744-227919244	A549	lung:	n/a	n/a
35	POLR2A	chr1:227915637-227919482	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:227917695-227919551	K562	blood:	n/a	n/a
37	POLR2A	chr1:227916264-227920310	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:227915774-227919906	K562	blood:	n/a	n/a
39	POLR2A	chr1:227915672-227920956	HEK293	kidney:	n/a	n/a
40	POLR2A	chr1:227916111-227919736	GM12892	blood:	n/a	n/a
41	POLR2A	chr1:227915694-227919622	Raji	blood:	n/a	n/a
42	POLR2A	chr1:227916255-227921984	K562	blood:	n/a	n/a
43	POLR2A	chr1:227916428-227919480	K562	blood:	n/a	n/a
44	MAX	chr1:227916271-227919285	HepG2	liver:	n/a	chr1:227917973-227917984 chr1:227916733-227916742 chr1:227917511-227917520
45	POLR2A	chr1:227915629-227920059	HL-60	blood:	n/a	n/a
46	POLR2A	chr1:227919037-227919521	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:227916827-227921915	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:227915635-227919479	HL-60	blood:	n/a	n/a
49	POLR2A	chr1:227916932-227919929	GM12891	blood:	n/a	n/a
50	POLR2A	chr1:227916248-227922017	SK-N-MC	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227916734..227919516-chr1:228336405..228338652,2	MCF-7	breast:
2	chr1:227917727..227921370-chr1:227944241..227947517,4	MCF-7	breast:
3	chr1:227917332..227919263-chr20:52209333..52211800,2	MCF-7	breast:
4	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
5	chr1:227917861..227920741-chr1:228675887..228677861,2	MCF-7	breast:
6	chr1:227672982..227674850-chr1:227918666..227921281,2	MCF-7	breast:
7	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:

No data

Variant related genes	Relation type
SNAP47	TF binding region
ENSG00000171940	Chromatin interaction
ENSG00000230005	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000168159	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10799445	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916204	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12073225	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12077397	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12097239	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12127819	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12141801	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17555357	0.84[YRI][hapmap]
rs2236359	0.84[YRI][hapmap]
rs2295994	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs6664307	0.90[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3088389	JMJD4	cis	multi-tissue	Pritchard
rs3088389	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227916600-227919600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:227916800-227919400	Weak transcription	Aorta	Aorta
3	chr1:227916800-227919400	Weak transcription	Osteobl	bone
4	chr1:227916800-227921600	Weak transcription	HUVEC	blood vessel
5	chr1:227917000-227919200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:227917000-227919600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:227917000-227921000	Weak transcription	Hela-S3	cervix
8	chr1:227917000-227921800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:227917000-227921800	Weak transcription	Psoas Muscle	Psoas
10	chr1:227917200-227919200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:227917200-227919200	Enhancers	Pancreas	Pancrea
12	chr1:227917200-227919600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:227917200-227920400	Genic enhancers	Spleen	Spleen
14	chr1:227917200-227921400	Weak transcription	Fetal Brain Male	brain
15	chr1:227917200-227921400	Weak transcription	NH-A	brain
16	chr1:227917200-227921600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:227917200-227921600	Weak transcription	Stomach Mucosa	stomach
18	chr1:227917200-227922000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:227917400-227919600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:227917400-227919600	Weak transcription	GM12878-XiMat	blood
21	chr1:227917400-227921400	Weak transcription	Primary B cells from cord blood	blood
22	chr1:227917400-227921400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:227917600-227919400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:227917600-227919400	Enhancers	Liver	Liver
25	chr1:227917600-227919600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr1:227917600-227921400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:227917800-227919200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:227917800-227919400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:227917800-227920200	Strong transcription	Fetal Brain Female	brain
30	chr1:227917800-227921400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:227918000-227919200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:227918000-227919200	Weak transcription	Brain Angular Gyrus	brain
33	chr1:227918000-227919400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:227918000-227920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:227918000-227921600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:227918200-227919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:227918200-227919200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:227918200-227919200	Weak transcription	Fetal Thymus	thymus
39	chr1:227918200-227919200	Weak transcription	Lung	lung
40	chr1:227918200-227919600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:227918200-227919800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:227918200-227921200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:227918200-227921800	Genic enhancers	Fetal Muscle Leg	muscle
44	chr1:227918400-227919200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:227918400-227919200	Genic enhancers	Fetal Intestine Small	intestine
46	chr1:227918400-227919600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:227918400-227919800	Strong transcription	Dnd41	blood
48	chr1:227918400-227921000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:227918400-227921200	Strong transcription	Fetal Stomach	stomach
50	chr1:227918400-227921200	Strong transcription	Thymus	Thymus

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