Variant report

Variant	rs786423
Chromosome Location	chr12:124083898-124083899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:124083541-124084062	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:124082990-124083946	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:124083814-124084181	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:124083741-124084580	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:124083859-124083974	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:124082972-124084214	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:124082678-124084635	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:124083359-124084090	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:124081632-124084546	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:124083661-124084206	GM12891	blood:	n/a	n/a
11	POLR2A	chr12:124082936-124084130	GM12892	blood:	n/a	n/a
12	POLR2A	chr12:124083818-124084314	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:124083671-124084051	K562	blood:	n/a	n/a
14	NFATC1	chr12:124083653-124083969	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:124082859-124084959	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr12:124082946-124084499	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:124083030-124084509	HepG2	liver:	n/a	n/a
18	POLR2A	chr12:124083762-124084191	HCT-116	colon:	n/a	n/a
19	POLR2A	chr12:124080492-124084849	K562	blood:	n/a	n/a
20	POLR2A	chr12:124083786-124084449	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr12:124083004-124084250	GM12891	blood:	n/a	n/a
22	POLR2A	chr12:124083749-124084025	MCF-7	breast:	n/a	n/a
23	POLR2A	chr12:124082907-124084808	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr12:124082908-124084597	GM12891	blood:	n/a	n/a
25	POLR2A	chr12:124083770-124084410	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr12:124083793-124084117	GM12878	blood:	n/a	n/a
27	MTA3	chr12:124083833-124084623	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:124083736-124084230	HepG2	liver:	n/a	n/a
29	HEY1	chr12:124083648-124084026	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:124082865-124084612	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr12:124083645-124084239	K562	blood:	n/a	n/a
32	POLR2A	chr12:124082950-124084340	U87	brain:	n/a	n/a
33	POLR2A	chr12:124083537-124084305	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr12:124082857-124085456	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:124083355-124084361	U87	brain:	n/a	n/a
36	POLR2A	chr12:124083712-124084591	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr12:124083671-124084050	K562	blood:	n/a	n/a
38	POLR2A	chr12:124083762-124084089	U87	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:124065661..124069328-chr12:124081746..124084446,4	K562	blood:
2	chr12:124081195..124083992-chr12:124117533..124119708,3	MCF-7	breast:
3	chr12:124075051..124078239-chr12:124079848..124084285,5	K562	blood:
4	chr12:123752131..123754716-chr12:124081309..124084264,2	MCF-7	breast:
5	chr12:124069965..124078255-chr12:124078837..124084347,12	K562	blood:

No data

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000111358	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000111361	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10846531	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs10846535	0.81[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11057307	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057320	0.80[EUR][1000 genomes]
rs11615300	0.81[EUR][1000 genomes]
rs1515814	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048802	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs3748268	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs3748269	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488883	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134896	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137946	0.81[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs7139193	0.81[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs7302183	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313628	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786422	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786444	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7958693	0.81[CEU][hapmap]
rs7966867	0.81[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs7966882	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7972413	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs884892	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs908373	0.82[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9919	0.83[GIH][hapmap]

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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs786423	DDX55	cis	multi-tissue	Pritchard
rs786423	TCTN2	cis	Artery Tibial	GTEx
rs786423	TCTN2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124070600-124084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:124071200-124084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:124071200-124084000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:124071200-124084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:124071600-124084400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr12:124072200-124085800	Weak transcription	Small Intestine	intestine
8	chr12:124072800-124084200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:124073200-124084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:124073400-124084000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:124073800-124084200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:124073800-124084600	Strong transcription	Fetal Thymus	thymus
13	chr12:124073800-124085200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:124073800-124085400	Weak transcription	Stomach Mucosa	stomach
15	chr12:124074000-124084400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:124074200-124086000	Weak transcription	Fetal Heart	heart
17	chr12:124075000-124084000	Strong transcription	Brain Substantia Nigra	brain
18	chr12:124075000-124084200	Strong transcription	Dnd41	blood
19	chr12:124075200-124085600	Weak transcription	Right Ventricle	heart
20	chr12:124075200-124085800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:124075200-124086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:124075200-124086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:124076800-124084000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:124076800-124085600	Weak transcription	Pancreas	Pancrea
25	chr12:124077000-124085600	Weak transcription	Spleen	Spleen
26	chr12:124077000-124086200	Weak transcription	Aorta	Aorta
27	chr12:124077400-124086000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:124077400-124086000	Weak transcription	Fetal Brain Male	brain
29	chr12:124078400-124085600	Weak transcription	Esophagus	oesophagus
30	chr12:124078600-124085200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:124078600-124085400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:124078800-124084200	Strong transcription	HSMM	muscle
33	chr12:124079000-124084200	Strong transcription	Fetal Lung	lung
34	chr12:124079000-124084400	Strong transcription	Primary T cells from cord blood	blood
35	chr12:124079400-124085400	Weak transcription	Fetal Intestine Small	intestine
36	chr12:124079400-124085600	Weak transcription	Fetal Stomach	stomach
37	chr12:124079400-124085600	Weak transcription	Lung	lung
38	chr12:124079800-124084000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:124079800-124084200	Strong transcription	K562	blood
40	chr12:124080000-124085800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:124080600-124086000	Weak transcription	Ovary	ovary
42	chr12:124081200-124084000	Strong transcription	Brain Hippocampus Middle	brain
43	chr12:124081800-124085400	Weak transcription	Colonic Mucosa	Colon
44	chr12:124081800-124085600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:124082000-124085400	Weak transcription	Primary B cells from cord blood	blood
46	chr12:124082000-124085600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:124082000-124086000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr12:124082200-124084000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:124082200-124085400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:124082200-124085400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links