Variant report

Variant	rs61955196
Chromosome Location	chr12:123451018-123451019
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123450717-123451133	A549	lung:	n/a	n/a
2	POLR2A	chr12:123450418-123451224	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr12:123450742-123451110	Raji	blood:	n/a	n/a
4	CTCF	chr12:123450880-123451030	AG04449	skin:	n/a	n/a
5	POLR2A	chr12:123450721-123451323	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:123450812-123451037	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP1	chr12:123450899-123451420	H1-hESC	embryonic stem cell:	n/a	chr12:123451103-123451113 chr12:123450963-123450972 chr12:123451142-123451153 chr12:123451059-123451071 chr12:123451038-123451047 chr12:123451202-123451211 chr12:123451061-123451070 chr12:123451036-123451048 chr12:123451060-123451069 chr12:123451059-123451071 chr12:123451038-123451047 chr12:123451099-123451113 chr12:123450962-123450971 chr12:123451037-123451046 chr12:123451061-123451070 chr12:123451144-123451153 chr12:123451036-123451048 chr12:123451102-123451114 chr12:123451102-123451114 chr12:123451056-123451070 chr12:123451202-123451211 chr12:123451201-123451211 chr12:123451144-123451153 chr12:123451200-123451212 chr12:123451142-123451154 chr12:123451197-123451211 chr12:123451104-123451113 chr12:123451103-123451112 chr12:123451142-123451154 chr12:123451200-123451212 chr12:123451104-123451113 chr12:123451201-123451211 chr12:123450962-123450976 chr12:123451143-123451152 chr12:123451075-123451084 chr12:123451070-123451083 chr12:123451201-123451210 chr12:123451103-123451113
8	CTCF	chr12:123450900-123451050	AG10803	skin:	n/a	n/a
9	REST	chr12:123450127-123451407	H1-neurons	neurons:	n/a	chr12:123450943-123450961 chr12:123450931-123450944 chr12:123450894-123450912
10	SMARCB1	chr12:123450317-123451380	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr12:123450840-123451313	GM12878	blood:	n/a	chr12:123450845-123450856 chr12:123451058-123451068 chr12:123451158-123451168
12	TAF1	chr12:123450772-123451069	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr12:123450738-123451126	NB4	blood:	n/a	n/a
14	MAX	chr12:123450400-123451276	A549	lung:	n/a	chr12:123450845-123450856 chr12:123451058-123451068 chr12:123451158-123451168
15	UBTF	chr12:123450812-123451096	K562	blood:	n/a	n/a
16	POLR2A	chr12:123450559-123451214	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr12:123450713-123451104	HepG2	liver:	n/a	n/a
18	EP300	chr12:123450725-123451192	HepG2	liver:	n/a	chr12:123450976-123450992 chr12:123450972-123450988
19	POLR2A	chr12:123450717-123451150	A549	lung:	n/a	n/a
20	MTA3	chr12:123450532-123451067	GM12878	blood:	n/a	n/a
21	MAX	chr12:123450760-123451490	H1-hESC	embryonic stem cell:	n/a	chr12:123450845-123450856 chr12:123451058-123451068 chr12:123451158-123451168
22	JUND	chr12:123450809-123451261	K562	blood:	n/a	chr12:123450964-123450973
23	CCNT2	chr12:123450296-123451334	K562	blood:	n/a	chr12:123451060-123451069 chr12:123451103-123451112 chr12:123451201-123451210
24	POLR2A	chr12:123450628-123451240	ProgFib	skin:	n/a	n/a
25	MXI1	chr12:123450774-123451409	HepG2	liver:	n/a	n/a
26	SMC3	chr12:123450770-123451019	K562	blood:	n/a	n/a
27	MAZ	chr12:123450610-123451390	K562	blood:	n/a	chr12:123450845-123450856 chr12:123451058-123451068 chr12:123451158-123451168
28	POLR2A	chr12:123450735-123451072	SK-N-MC	brain:	n/a	n/a
29	CEBPD	chr12:123450720-123451125	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:123450755-123451025	HepG2	liver:	n/a	n/a
31	TAF1	chr12:123450441-123451209	H1-neurons	neurons:	n/a	n/a
32	FOXP2	chr12:123450748-123451055	SK-N-MC	brain:	n/a	n/a
33	MAX	chr12:123450547-123451168	A549	lung:	n/a	chr12:123450845-123450856 chr12:123451058-123451068 chr12:123451158-123451168
34	TAF1	chr12:123450707-123451160	A549	lung:	n/a	n/a
35	TAF1	chr12:123450812-123451147	SK-N-SH	brain:	n/a	n/a
36	HMGN3	chr12:123450390-123451369	K562	blood:	n/a	n/a
37	STAT3	chr12:123450983-123451273	MCF10A-Er-Src	breast:	n/a	chr12:123451100-123451112
38	POLR2A	chr12:123450661-123451421	ECC-1	luminal epithelium:	n/a	n/a
39	IRF1	chr12:123450768-123451347	K562	blood:	n/a	chr12:123451036-123451050 chr12:123451142-123451156 chr12:123450959-123450973 chr12:123451200-123451214 chr12:123451102-123451116 chr12:123451059-123451073
40	RAD21	chr12:123450885-123451069	K562	blood:	n/a	n/a
41	RCOR1	chr12:123450574-123451139	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr12:123450642-123451271	MCF-7	breast:	n/a	n/a
43	POLR2A	chr12:123450722-123451096	Hela-S3	cervix:	n/a	n/a
44	SIN3AK20	chr12:123450826-123451047	HepG2	liver:	n/a	n/a
45	POLR2A	chr12:123450741-123451121	K562	blood:	n/a	n/a
46	ZNF143	chr12:123450543-123451234	H1-hESC	embryonic stem cell:	n/a	chr12:123450656-123450674 chr12:123451093-123451111 chr12:123450954-123450972
47	BRCA1	chr12:123450922-123451083	Hela-S3	cervix:	n/a	n/a
48	MYC	chr12:123450874-123451059	MCF-7	breast:	n/a	n/a
49	ZEB1	chr12:123450459-123451666	HepG2	liver:	n/a	chr12:123451228-123451235 chr12:123450848-123450855 chr12:123451332-123451343
50	BHLHE40	chr12:123450765-123451049	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123428831..123431560-chr12:123448558..123451555,2	K562	blood:
2	chr12:123318760..123321217-chr12:123449684..123452450,2	K562	blood:
3	chr12:123449701..123452611-chr12:123716445..123719411,3	K562	blood:
4	chr12:123443368..123448710-chr12:123448756..123452152,6	MCF-7	breast:
5	chr12:123319262..123321924-chr12:123450152..123453465,3	K562	blood:
6	chr12:123355640..123358495-chr12:123449218..123452212,2	MCF-7	breast:
7	chr12:123428831..123432471-chr12:123448558..123452277,3	K562	blood:
8	chr12:123450564..123451345-chr15:90727982..90728518,2	Hela-S3	cervix:
9	chr12:123449477..123453379-chr12:123715163..123718004,4	MCF-7	breast:
10	chr12:123449665..123451282-chr12:123753748..123757462,3	MCF-7	breast:
11	chr12:123449332..123452871-chr12:123717386..123719515,4	K562	blood:
12	chr12:122983924..122985565-chr12:123450706..123452240,2	MCF-7	breast:
13	chr12:123373192..123374846-chr12:123449556..123451152,2	MCF-7	breast:

Variant related genes	Relation type
ABCB9	TF binding region
ENSG00000185033	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10773921	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11060853	0.88[ASN][1000 genomes]
rs11608811	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11613937	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12425009	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12425850	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1984658	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28755851	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741530	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759115	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3897102	0.95[ASN][1000 genomes]
rs4148866	0.87[ASN][1000 genomes]
rs4275659	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55742290	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61955214	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7135296	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7296418	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305511	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957096	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs883562	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884956	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs61955196	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs61955196	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs61955196	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs61955196	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs61955196	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs61955196	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123446000-123451400	Enhancers	Fetal Heart	heart
2	chr12:123449800-123451400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:123449800-123451400	Active TSS	Osteobl	bone
4	chr12:123450000-123451200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr12:123450000-123451400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:123450000-123451400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:123450000-123451400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:123450200-123451200	Active TSS	Fetal Brain Female	brain
9	chr12:123450200-123451200	Active TSS	HepG2	liver
10	chr12:123450200-123451400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:123450200-123451400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr12:123450200-123451600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:123450200-123451800	Active TSS	A549	lung
14	chr12:123450200-123451800	Active TSS	Hela-S3	cervix
15	chr12:123450400-123451200	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:123450400-123451400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr12:123450400-123451400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:123450400-123451400	Active TSS	Fetal Kidney	kidney
19	chr12:123450400-123451600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr12:123450600-123451200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr12:123450600-123451200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:123450600-123451200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:123450600-123451200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr12:123450600-123451200	Active TSS	Brain Angular Gyrus	brain
25	chr12:123450600-123451200	Active TSS	Fetal Intestine Large	intestine
26	chr12:123450600-123451200	Active TSS	Ovary	ovary
27	chr12:123450600-123451200	Active TSS	K562	blood
28	chr12:123450600-123451200	Active TSS	NHEK	skin
29	chr12:123450600-123451400	Active TSS	Brain Anterior Caudate	brain
30	chr12:123450600-123451400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr12:123450600-123451400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:123450600-123451400	Active TSS	Brain Substantia Nigra	brain
33	chr12:123450800-123451200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:123450800-123451200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:123450800-123451200	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr12:123450800-123451200	Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr12:123450800-123451200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:123450800-123451200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:123450800-123451200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:123450800-123451200	Active TSS	Brain Cingulate Gyrus	brain
41	chr12:123450800-123451200	Active TSS	Brain Hippocampus Middle	brain
42	chr12:123450800-123451200	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr12:123450800-123451200	Transcr. at gene 5' and 3'	Right Atrium	heart
44	chr12:123450800-123451200	Active TSS	Thymus	Thymus
45	chr12:123450800-123451400	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr12:123450800-123451400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr12:123450800-123451400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:123450800-123451400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:123450800-123451400	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr12:123451000-123451200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links