Variant report

Variant	rs28397122
Chromosome Location	chr12:123848896-123848897
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	chr12:123848448-123850525	GM12878	blood:	n/a	n/a
2	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
3	MTA3	chr12:123848126-123848967	GM12878	blood:	n/a	n/a
4	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
5	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
6	TAF1	chr12:123848852-123849604	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:123848299-123848974	Hela-S3	cervix:	n/a	n/a
8	SIN3AK20	chr12:123848829-123850552	SK-N-SH	brain:	n/a	n/a
9	RELA	chr12:123848794-123850568	GM15510	blood:	n/a	n/a
10	ELF1	chr12:123848751-123849088	K562	blood:	n/a	chr12:123849009-123849021 chr12:123848783-123848795
11	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
12	TAF1	chr12:123848836-123850604	A549	lung:	n/a	n/a
13	POLR2A	chr12:123848798-123849430	PBDE	blood:	n/a	n/a
14	MXI1	chr12:123847757-123849417	GM12878	blood:	n/a	n/a
15	ZBTB7A	chr12:123848472-123849064	ECC-1	luminal epithelium:	n/a	chr12:123848893-123848900
16	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
17	CTCF	chr12:123848820-123848970	SAEC	small airway:	n/a	n/a
18	MAX	chr12:123847824-123848951	MCF-7	breast:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
19	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
20	POLR2A	chr12:123847947-123850576	GM12878	blood:	n/a	n/a
21	YY1	chr12:123848496-123850280	K562	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
22	POLR2A	chr12:123848159-123850570	GM12892	blood:	n/a	n/a
23	POLR2A	chr12:123848590-123849017	GM12878	blood:	n/a	n/a
24	REST	chr12:123848883-123850579	HL-60	blood:	n/a	chr12:123849144-123849157
25	UBTF	chr12:123848640-123849398	K562	blood:	n/a	n/a
26	MXI1	chr12:123847986-123850551	HepG2	liver:	n/a	n/a
27	MAX	chr12:123847753-123848984	HCT-116	colon:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
28	TAF1	chr12:123848515-123850310	ECC-1	luminal epithelium:	n/a	n/a
29	NR2F2	chr12:123847703-123848999	K562	blood:	n/a	chr12:123848103-123848118
30	MAZ	chr12:123848537-123850591	GM12878	blood:	n/a	chr12:123849752-123849761 chr12:123849752-123849761 chr12:123849752-123849761 chr12:123849747-123849766 chr12:123849750-123849763
31	POLR2A	chr12:123848503-123850293	A549	lung:	n/a	n/a
32	REST	chr12:123848818-123850688	A549	lung:	n/a	chr12:123849144-123849157 chr12:123848865-123848875
33	CCNT2	chr12:123848629-123850290	K562	blood:	n/a	chr12:123849719-123849728 chr12:123849390-123849399
34	ZBTB7A	chr12:123848765-123849983	K562	blood:	n/a	chr12:123848893-123848900
35	MAX	chr12:123847743-123848974	A549	lung:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
36	MAX	chr12:123847814-123850548	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
37	MYC	chr12:123847800-123848974	A549	lung:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
38	RELA	chr12:123848831-123850583	GM12891	blood:	n/a	n/a
39	MXI1	chr12:123847579-123850676	IMR90	lung:	n/a	n/a
40	CHD1	chr12:123847901-123850607	GM12878	blood:	n/a	chr12:123849894-123849904 chr12:123849133-123849143
41	TAF1	chr12:123848728-123849038	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr12:123848565-123850530	NB4	blood:	n/a	n/a
43	MXI1	chr12:123847099-123850811	SK-N-SH	brain:	n/a	n/a
44	YY1	chr12:123848871-123849658	GM12891	blood:	n/a	chr12:123849082-123849096 chr12:123849371-123849380 chr12:123849378-123849386 chr12:123849374-123849386 chr12:123849376-123849384 chr12:123849372-123849392 chr12:123849375-123849385 chr12:123849375-123849397
45	TAF1	chr12:123848156-123848936	H1-hESC	embryonic stem cell:	n/a	n/a
46	BHLHE40	chr12:123848026-123850593	GM12878	blood:	n/a	chr12:123849746-123849767 chr12:123849751-123849760 chr12:123849752-123849761 chr12:123849753-123849762 chr12:123849750-123849763 chr12:123849752-123849761
47	MYC	chr12:123847850-123848925	K562	blood:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
48	MAX	chr12:123847848-123848942	ECC-1	luminal epithelium:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
49	POLR2A	chr12:123848352-123848961	H1-hESC	embryonic stem cell:	n/a	n/a
50	YY1	chr12:123848566-123850498	GM12878	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

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	chr12:123848585..123850676-chr17:56707936..56709681,2	MCF-7	breast:
4	chr12:123847805..123850449-chr12:124195534..124198038,2	K562	blood:
5	chr12:123754032..123756441-chr12:123848296..123851530,6	K562	blood:
6	chr12:123847748..123850760-chr12:123875045..123877875,5	MCF-7	breast:
7	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
8	chr12:123846880..123851536-chr12:123865445..123870876,12	MCF-7	breast:
9	chr12:123848299..123850965-chr15:65596079..65598370,2	MCF-7	breast:
10	chr12:123846861..123850261-chr12:124066655..124071408,9	MCF-7	breast:
11	chr12:123847204..123849398-chr12:123874460..123876425,2	K562	blood:
12	chr12:123833002..123837136-chr12:123847313..123849620,3	MCF-7	breast:
13	chr12:123832815..123836496-chr12:123847723..123851604,4	MCF-7	breast:
14	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
15	chr12:123847713..123850022-chr12:124067528..124071055,3	MCF-7	breast:
16	chr12:123847169..123849970-chr12:124085128..124088523,3	K562	blood:
17	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:
18	chr12:123846000..123850093-chr12:124067189..124070124,4	K562	blood:
19	chr12:123753451..123758032-chr12:123846651..123850459,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SETD8-1	chr12:123848415-123850334	ENSG00000256092.2

Variant related genes	Relation type
ENSG00000256092	TF binding region
ENSG00000111328	Chromatin interaction
ENSG00000207189	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000185344	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000111361	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	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10773009	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773010	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773014	0.91[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[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846510	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846511	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846514	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846518	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846521	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846522	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846524	0.91[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[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[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057285	0.91[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[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376696	0.95[ASN][1000 genomes]
rs28377694	1.00[ASN][1000 genomes]
rs28454135	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28475177	0.91[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	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28655516	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660661	0.85[AFR][1000 genomes];1.00[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	0.91[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	0.91[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	0.91[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
rs28397122	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	chr12:123847200-123850600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:123847400-123849000	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr12:123847400-123850400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr12:123847400-123850600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:123847400-123850600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:123847400-123850600	Active TSS	Right Ventricle	heart
7	chr12:123847400-123850800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:123847600-123849200	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr12:123847600-123850400	Active TSS	Aorta	Aorta
10	chr12:123847600-123850600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:123847600-123850600	Active TSS	Psoas Muscle	Psoas
12	chr12:123847600-123850600	Active TSS	NHLF	lung
13	chr12:123847800-123850000	Active TSS	HSMM	muscle
14	chr12:123847800-123850000	Active TSS	HSMMtube	muscle
15	chr12:123847800-123850400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:123847800-123850600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr12:123847800-123850600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr12:123847800-123850600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr12:123847800-123850600	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:123847800-123850600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:123847800-123850600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:123847800-123850600	Active TSS	Fetal Muscle Trunk	muscle
23	chr12:123847800-123850600	Active TSS	Right Atrium	heart
24	chr12:123847800-123850800	Active TSS	GM12878-XiMat	blood
25	chr12:123848000-123849400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:123848000-123850400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:123848000-123850400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:123848000-123850400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:123848000-123850400	Active TSS	Ovary	ovary
30	chr12:123848000-123850400	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr12:123848000-123850600	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr12:123848000-123850600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr12:123848000-123850600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:123848000-123850600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:123848000-123850600	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr12:123848000-123850600	Active TSS	Colon Smooth Muscle	Colon
37	chr12:123848000-123850600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:123848000-123850600	Active TSS	Fetal Intestine Large	intestine
39	chr12:123848000-123850600	Active TSS	Fetal Intestine Small	intestine
40	chr12:123848000-123850600	Active TSS	A549	lung
41	chr12:123848000-123850800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:123848000-123850800	Active TSS	Fetal Kidney	kidney
43	chr12:123848000-123850800	Active TSS	Thymus	Thymus
44	chr12:123848200-123849000	Active TSS	Fetal Brain Male	brain
45	chr12:123848200-123850000	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr12:123848200-123850000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:123848200-123850000	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr12:123848200-123850000	Active TSS	Stomach Mucosa	stomach
49	chr12:123848200-123850000	Active TSS	HMEC	breast
50	chr12:123848200-123850000	Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links