Variant report

Variant	rs61955088
Chromosome Location	chr12:123850541-123850542
allele	A/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	chr12:123849063-123850614	PANC-1	pancreas:	n/a	n/a
2	CTCF	chr12:123850162-123850622	IMR90	lung:	n/a	chr12:123850402-123850423 chr12:123850407-123850425
3	PML	chr12:123849614-123850634	K562	blood:	n/a	n/a
4	CUX1	chr12:123849695-123850596	GM12878	blood:	n/a	n/a
5	NRF1	chr12:123849281-123850572	GM12878	blood:	n/a	chr12:123849886-123849897 chr12:123849886-123849900 chr12:123849448-123849457 chr12:123849886-123849895 chr12:123849888-123849897 chr12:123849885-123849896 chr12:123849883-123849897
6	ZNF143	chr12:123849619-123850564	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr12:123849626-123850542	Hela-S3	cervix:	n/a	n/a
8	TBP	chr12:123849138-123850611	GM12878	blood:	n/a	n/a
9	MXI1	chr12:123849199-123850558	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr12:123849727-123850730	GM12878	blood:	n/a	n/a
11	MYC	chr12:123847917-123850577	NB4	blood:	n/a	chr12:123849752-123849761 chr12:123848142-123848149 chr12:123849752-123849761 chr12:123849752-123849761 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123849747-123849766 chr12:123848140-123848155 chr12:123849750-123849763
12	RAD21	chr12:123850077-123850637	A549	lung:	n/a	chr12:123850405-123850424
13	CTCF	chr12:123850304-123850546	Kidney_OC	kidney:	n/a	chr12:123850402-123850423 chr12:123850407-123850425
14	CTCF	chr12:123850315-123850548	LNCaP	prostate:	n/a	chr12:123850402-123850423 chr12:123850407-123850425
15	ATF2	chr12:123849458-123850671	GM12878	blood:	n/a	n/a
16	SIN3A	chr12:123847827-123850593	H1-hESC	embryonic stem cell:	n/a	chr12:123849267-123849280 chr12:123848960-123848973 chr12:123849753-123849762 chr12:123849273-123849281 chr12:123849751-123849760
17	BHLHE40	chr12:123849138-123850573	K562	blood:	n/a	chr12:123849746-123849767 chr12:123849751-123849760 chr12:123849752-123849761 chr12:123849753-123849762 chr12:123849750-123849763 chr12:123849752-123849761
18	MXI1	chr12:123849621-123850596	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:123849058-123850599	SK-N-MC	brain:	n/a	n/a
20	MAX	chr12:123849111-123850598	A549	lung:	n/a	chr12:123849752-123849761 chr12:123849752-123849761 chr12:123849752-123849761 chr12:123849747-123849766 chr12:123849750-123849763
21	CTCF	chr12:123850280-123850551	LNCaP	prostate:	n/a	chr12:123850402-123850423 chr12:123850407-123850425
22	SP1	chr12:123849589-123850605	GM12878	blood:	n/a	chr12:123849715-123849729 chr12:123849719-123849728 chr12:123849718-123849730
23	CTCF	chr12:123850161-123850541	A549	lung:	n/a	chr12:123850402-123850423 chr12:123850407-123850425
24	POLR2A	chr12:123849545-123850583	HL-60	blood:	n/a	n/a
25	MAFK	chr12:123849747-123850575	K562	blood:	n/a	n/a
26	PAX5	chr12:123850100-123850578	GM12891	blood:	n/a	chr12:123850263-123850272
27	EP300	chr12:123849604-123850585	GM12878	blood:	n/a	chr12:123850263-123850277
28	POLR2A	chr12:123849069-123850566	H1-neurons	neurons:	n/a	n/a
29	JUND	chr12:123849200-123850561	K562	blood:	n/a	chr12:123850265-123850274 chr12:123850348-123850360
30	POLR2A	chr12:123849109-123850561	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:123848979-123850612	GM12892	blood:	n/a	n/a
32	SIN3AK20	chr12:123848829-123850552	SK-N-SH	brain:	n/a	n/a
33	RELA	chr12:123848794-123850568	GM15510	blood:	n/a	n/a
34	MAX	chr12:123847933-123850552	K562	blood:	n/a	chr12:123849752-123849761 chr12:123848142-123848149 chr12:123849752-123849761 chr12:123849752-123849761 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123849747-123849766 chr12:123848140-123848155 chr12:123849750-123849763
35	POLR2A	chr12:123849057-123850553	GM12891	blood:	n/a	n/a
36	TAF1	chr12:123848836-123850604	A549	lung:	n/a	n/a
37	E2F4	chr12:123849204-123850545	K562	blood:	n/a	chr12:123849887-123849896 chr12:123849262-123849272 chr12:123849804-123849815 chr12:123850123-123850138 chr12:123849801-123849816 chr12:123849585-123849592 chr12:123849371-123849380
38	CTCF	chr12:123850154-123850574	K562	blood:	n/a	chr12:123850402-123850423 chr12:123850407-123850425
39	MAX	chr12:123849240-123850564	H1-hESC	embryonic stem cell:	n/a	chr12:123849752-123849761 chr12:123849752-123849761 chr12:123849752-123849761 chr12:123849747-123849766 chr12:123849750-123849763
40	POLR2A	chr12:123849132-123850542	K562	blood:	n/a	n/a
41	NFIC	chr12:123849710-123850698	GM12878	blood:	n/a	n/a
42	CHD2	chr12:123849128-123850543	Hela-S3	cervix:	n/a	chr12:123849894-123849904 chr12:123849133-123849143
43	POLR2A	chr12:123849098-123850661	GM12878	blood:	n/a	n/a
44	ATF3	chr12:123849656-123850574	A549	lung:	n/a	chr12:123849752-123849761 chr12:123849702-123849710
45	WRNIP1	chr12:123849626-123850553	GM12878	blood:	n/a	n/a
46	STAT5A	chr12:123849789-123850636	K562	blood:	n/a	n/a
47	MYBL2	chr12:123849483-123850688	HepG2	liver:	n/a	n/a
48	MAX	chr12:123849079-123850610	HepG2	liver:	n/a	chr12:123849752-123849761 chr12:123849752-123849761 chr12:123849752-123849761 chr12:123849747-123849766 chr12:123849750-123849763
49	EBF1	chr12:123849720-123850569	GM12878	blood:	n/a	n/a
50	POLR2A	chr12:123849035-123850581	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123849365..123850946-chr12:123941525..123944430,2	K562	blood:
2	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:
3	chr12:123848585..123850676-chr17:56707936..56709681,2	MCF-7	breast:
4	chr12:123756475..123758463-chr12:123849452..123851589,2	K562	blood:
5	chr12:123754032..123756441-chr12:123848296..123851530,6	K562	blood:
6	chr12:123849812..123851534-chr12:123858422..123861381,2	MCF-7	breast:
7	chr12:123847748..123850760-chr12:123875045..123877875,5	MCF-7	breast:
8	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
9	chr12:123846880..123851536-chr12:123865445..123870876,12	MCF-7	breast:
10	chr12:123850101..123850661-chr20:30192047..30192923,2	Hela-S3	cervix:
11	chr12:123848299..123850965-chr15:65596079..65598370,2	MCF-7	breast:
12	chr12:123832815..123836496-chr12:123847723..123851604,4	MCF-7	breast:
13	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
14	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SETD8-1	chr12:123850072-123850660	ENSG00000256092

Variant related genes	Relation type
SBNO1	TF binding region
ENSG00000200156	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000207189	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10444447	0.82[ASN][1000 genomes]
rs10444448	0.82[ASN][1000 genomes]
rs10773007	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10773009	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773010	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773014	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846495	0.82[ASN][1000 genomes]
rs10846496	0.82[ASN][1000 genomes]
rs10846498	0.82[ASN][1000 genomes]
rs10846499	0.82[ASN][1000 genomes]
rs10846500	0.82[ASN][1000 genomes]
rs10846501	0.82[ASN][1000 genomes]
rs10846503	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10846504	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10846509	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846510	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846511	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846514	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846518	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846521	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846522	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846524	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057231	0.82[ASN][1000 genomes]
rs11057240	0.82[ASN][1000 genomes]
rs11057243	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11057250	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11057264	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057266	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057285	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057286	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371973	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376696	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28377694	1.00[ASN][1000 genomes]
rs28397122	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454135	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28475177	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573826	1.00[ASN][1000 genomes]
rs28633324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28646185	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28655516	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660661	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861152	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281511	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4313613	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61953413	0.82[ASN][1000 genomes]
rs61955089	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61955114	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61955117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488868	1.00[ASN][1000 genomes]
rs73231946	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	esv3371959	chr12:123848399-123850847	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61955088	CDK2AP1	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123847200-123850600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:123847400-123850600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:123847400-123850600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:123847400-123850600	Active TSS	Right Ventricle	heart
5	chr12:123847400-123850800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:123847600-123850600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:123847600-123850600	Active TSS	Psoas Muscle	Psoas
8	chr12:123847600-123850600	Active TSS	NHLF	lung
9	chr12:123847800-123850600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr12:123847800-123850600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr12:123847800-123850600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:123847800-123850600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr12:123847800-123850600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:123847800-123850600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:123847800-123850600	Active TSS	Fetal Muscle Trunk	muscle
16	chr12:123847800-123850600	Active TSS	Right Atrium	heart
17	chr12:123847800-123850800	Active TSS	GM12878-XiMat	blood
18	chr12:123848000-123850600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:123848000-123850600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr12:123848000-123850600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:123848000-123850600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:123848000-123850600	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr12:123848000-123850600	Active TSS	Colon Smooth Muscle	Colon
24	chr12:123848000-123850600	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr12:123848000-123850600	Active TSS	Fetal Intestine Large	intestine
26	chr12:123848000-123850600	Active TSS	Fetal Intestine Small	intestine
27	chr12:123848000-123850600	Active TSS	A549	lung
28	chr12:123848000-123850800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:123848000-123850800	Active TSS	Fetal Kidney	kidney
30	chr12:123848000-123850800	Active TSS	Thymus	Thymus
31	chr12:123848200-123850600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:123848200-123850600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:123848200-123850600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:123848200-123850600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:123848200-123850600	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr12:123848200-123850600	Active TSS	Colonic Mucosa	Colon
37	chr12:123848200-123850600	Active TSS	Lung	lung
38	chr12:123848200-123850600	Active TSS	Pancreas	Pancrea
39	chr12:123848200-123850600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr12:123848200-123850600	Active TSS	NHDF-Ad	bronchial
41	chr12:123848200-123850800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:123848200-123850800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr12:123848400-123850600	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr12:123848400-123850600	Active TSS	Brain Cingulate Gyrus	brain
45	chr12:123848400-123850600	Active TSS	Fetal Lung	lung
46	chr12:123848400-123850600	Active TSS	Fetal Stomach	stomach
47	chr12:123848400-123850600	Active TSS	Left Ventricle	heart
48	chr12:123848400-123850800	Active TSS	Stomach Smooth Muscle	stomach
49	chr12:123848400-123850800	Active TSS	Hela-S3	cervix
50	chr12:123848600-123850600	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links