Variant report

Variant	rs28660661
Chromosome Location	chr12:123848455-123848456
allele	A/C
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	SIN3AK20	chr12:123847953-123848629	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:123848448-123850525	GM12878	blood:	n/a	n/a
3	NFYB	chr12:123848004-123848481	GM12878	blood:	n/a	chr12:123848357-123848370
4	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
5	MTA3	chr12:123848126-123848967	GM12878	blood:	n/a	n/a
6	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
7	YY1	chr12:123848454-123850397	GM12892	blood:	n/a	chr12:123849082-123849096 chr12:123849822-123849831 chr12:123849371-123849380 chr12:123849378-123849386 chr12:123849374-123849386 chr12:123849376-123849384 chr12:123849372-123849392 chr12:123849375-123849385 chr12:123849375-123849397
8	MXI1	chr12:123847795-123848884	K562	blood:	n/a	n/a
9	POLR2A	chr12:123847866-123848719	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:123848299-123848974	Hela-S3	cervix:	n/a	n/a
11	SIN3AK20	chr12:123847916-123848852	A549	lung:	n/a	n/a
12	MYC	chr12:123848239-123848688	H1-hESC	embryonic stem cell:	n/a	n/a
13	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
14	PML	chr12:123847956-123848881	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr12:123847962-123848620	HepG2	liver:	n/a	n/a
16	MAX	chr12:123847805-123848755	SK-N-SH	brain:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
17	HEY1	chr12:123848266-123848633	HepG2	liver:	n/a	n/a
18	MXI1	chr12:123847757-123849417	GM12878	blood:	n/a	n/a
19	MAFK	chr12:123848301-123848523	K562	blood:	n/a	n/a
20	MAZ	chr12:123847840-123850579	IMR90	lung:	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
21	TBL1XR1	chr12:123847999-123848672	K562	blood:	n/a	n/a
22	TBP	chr12:123848293-123848622	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIN3AK20	chr12:123847748-123848822	K562	blood:	n/a	n/a
24	GABPA	chr12:123848015-123848527	A549	lung:	n/a	n/a
25	MAX	chr12:123847824-123848951	MCF-7	breast:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
26	STAT5A	chr12:123847908-123850691	GM12878	blood:	n/a	chr12:123848772-123848784 chr12:123848483-123848497 chr12:123848486-123848494 chr12:123848480-123848500 chr12:123849152-123849164 chr12:123849694-123849718 chr12:123849202-123849214 chr12:123848387-123848399
27	SIN3AK20	chr12:123847817-123848584	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:123848200-123848601	HepG2	liver:	n/a	n/a
29	MAX	chr12:123847939-123848457	K562	blood:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
30	TEAD4	chr12:123848126-123848614	HepG2	liver:	n/a	n/a
31	TAF1	chr12:123848303-123848547	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:123847947-123850576	GM12878	blood:	n/a	n/a
33	ZNF263	chr12:123847944-123848778	HEK293-T-REx	kidney:	n/a	chr12:123848392-123848401
34	WRNIP1	chr12:123847877-123848858	GM12878	blood:	n/a	n/a
35	BCL3	chr12:123847789-123848848	A549	lung:	n/a	chr12:123848680-123848693
36	ELF1	chr12:123847788-123848534	A549	lung:	n/a	chr12:123848160-123848169 chr12:123848158-123848171 chr12:123848159-123848170 chr12:123848159-123848170
37	POLR2A	chr12:123848159-123850570	GM12892	blood:	n/a	n/a
38	MAZ	chr12:123848153-123848751	K562	blood:	n/a	n/a
39	POLR2A	chr12:123848119-123848669	HUVEC	blood vessel:	n/a	n/a
40	MAX	chr12:123847937-123848726	H1-hESC	embryonic stem cell:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
41	POLR2A	chr12:123848079-123848808	Hela-S3	cervix:	n/a	n/a
42	MXI1	chr12:123847986-123850551	HepG2	liver:	n/a	n/a
43	MAFK	chr12:123848399-123848518	HepG2	liver:	n/a	n/a
44	MAX	chr12:123847753-123848984	HCT-116	colon:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
45	POLR2A	chr12:123848349-123848601	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr12:123847894-123848753	PANC-1	pancreas:	n/a	n/a
47	NR2F2	chr12:123847703-123848999	K562	blood:	n/a	chr12:123848103-123848118
48	POLR2A	chr12:123848113-123848885	K562	blood:	n/a	n/a
49	RAD21	chr12:123848402-123848829	IMR90	lung:	n/a	n/a
50	FOXA2	chr12:123848176-123848492	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123847301..123849584-chr12:124117443..124120110,3	K562	blood:
2	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:
3	chr12:123847805..123850449-chr12:124195534..124198038,2	K562	blood:
4	chr12:123754032..123756441-chr12:123848296..123851530,6	K562	blood:
5	chr12:123847748..123850760-chr12:123875045..123877875,5	MCF-7	breast:
6	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
7	chr12:123846880..123851536-chr12:123865445..123870876,12	MCF-7	breast:
8	chr12:123848299..123850965-chr15:65596079..65598370,2	MCF-7	breast:
9	chr12:123846861..123850261-chr12:124066655..124071408,9	MCF-7	breast:
10	chr12:123847204..123849398-chr12:123874460..123876425,2	K562	blood:
11	chr12:123833002..123837136-chr12:123847313..123849620,3	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	chr12:123847713..123850022-chr12:124067528..124071055,3	MCF-7	breast:
15	chr12:123847169..123849970-chr12:124085128..124088523,3	K562	blood:
16	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:
17	chr12:123846000..123850093-chr12:124067189..124070124,4	K562	blood:
18	chr12:123753451..123758032-chr12:123846651..123850459,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SETD8-1	chr12:123848356-123848554	NONHSAT031583
2	lnc-SETD8-1	chr12:123848415-123850334	ENSG00000256092.2
3	lnc-SETD8-1	chr12:123848415-123848554	NONHSAT031585

Variant related genes	Relation type
ENSG00000256092	TF binding region
ENSG00000111328	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000207189	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000185344	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	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10773009	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773010	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773014	0.94[AFR][1000 genomes];1.00[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	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10846504	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10846509	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846510	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846511	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846514	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846518	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846521	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846522	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846524	0.94[AFR][1000 genomes];1.00[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	0.91[ASN][1000 genomes]
rs11057250	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11057264	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057266	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057285	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057286	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371973	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376696	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28377694	1.00[ASN][1000 genomes]
rs28397122	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454135	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28475177	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573826	1.00[ASN][1000 genomes]
rs28633324	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28646185	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28655516	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861152	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898283	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281511	0.91[ASN][1000 genomes]
rs4313613	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61953413	0.82[ASN][1000 genomes]
rs61955088	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61955089	0.91[ASN][1000 genomes]
rs61955114	0.91[ASN][1000 genomes]
rs61955117	0.94[AFR][1000 genomes];0.96[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
rs28660661	CDK2AP1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123847000-123848800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:123847200-123848600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:123847200-123850600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:123847400-123848600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr12:123847400-123848600	Flanking Active TSS	Brain Germinal Matrix	brain
6	chr12:123847400-123848800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr12:123847400-123848800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:123847400-123849000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr12:123847400-123850400	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr12:123847400-123850600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:123847400-123850600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:123847400-123850600	Active TSS	Right Ventricle	heart
13	chr12:123847400-123850800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr12:123847600-123848600	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr12:123847600-123848600	Flanking Active TSS	HUVEC	blood vessel
16	chr12:123847600-123848600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr12:123847600-123848800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr12:123847600-123849200	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr12:123847600-123850400	Active TSS	Aorta	Aorta
20	chr12:123847600-123850600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr12:123847600-123850600	Active TSS	Psoas Muscle	Psoas
22	chr12:123847600-123850600	Active TSS	NHLF	lung
23	chr12:123847800-123848600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:123847800-123848600	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr12:123847800-123848600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:123847800-123848600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:123847800-123848600	Flanking Active TSS	Liver	Liver
28	chr12:123847800-123848600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr12:123847800-123848800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr12:123847800-123848800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr12:123847800-123848800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr12:123847800-123850000	Active TSS	HSMM	muscle
33	chr12:123847800-123850000	Active TSS	HSMMtube	muscle
34	chr12:123847800-123850400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:123847800-123850600	Active TSS	H1 Cell Line	embryonic stem cell
36	chr12:123847800-123850600	Active TSS	H9 Cell Line	embryonic stem cell
37	chr12:123847800-123850600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr12:123847800-123850600	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr12:123847800-123850600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:123847800-123850600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:123847800-123850600	Active TSS	Fetal Muscle Trunk	muscle
42	chr12:123847800-123850600	Active TSS	Right Atrium	heart
43	chr12:123847800-123850800	Active TSS	GM12878-XiMat	blood
44	chr12:123848000-123848600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:123848000-123848600	Bivalent/Poised TSS	HepG2	liver
46	chr12:123848000-123848800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr12:123848000-123848800	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr12:123848000-123848800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr12:123848000-123848800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr12:123848000-123849400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links