Variant report

Variant	rs28553365
Chromosome Location	chr12:123847841-123847842
allele	C/T
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	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
2	MXI1	chr12:123847795-123848884	K562	blood:	n/a	n/a
3	MAX	chr12:123847805-123848755	SK-N-SH	brain:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
4	MXI1	chr12:123847757-123849417	GM12878	blood:	n/a	n/a
5	USF2	chr12:123847793-123848310	GM12878	blood:	n/a	n/a
6	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
7	SIN3AK20	chr12:123847748-123848822	K562	blood:	n/a	n/a
8	MAX	chr12:123847824-123848951	MCF-7	breast:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
9	SIN3AK20	chr12:123847817-123848584	MCF-7	breast:	n/a	n/a
10	BCL3	chr12:123847789-123848848	A549	lung:	n/a	chr12:123848680-123848693
11	ELF1	chr12:123847788-123848534	A549	lung:	n/a	chr12:123848160-123848169 chr12:123848158-123848171 chr12:123848159-123848170 chr12:123848159-123848170
12	USF1	chr12:123847810-123848435	HCT-116	colon:	n/a	n/a
13	MAX	chr12:123847753-123848984	HCT-116	colon:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
14	NR2F2	chr12:123847703-123848999	K562	blood:	n/a	chr12:123848103-123848118
15	NR2F2	chr12:123847749-123848619	K562	blood:	n/a	chr12:123848103-123848118
16	MAX	chr12:123847743-123848974	A549	lung:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
17	SIN3AK20	chr12:123847755-123848667	A549	lung:	n/a	n/a
18	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
19	MYC	chr12:123847800-123848974	A549	lung:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
20	MXI1	chr12:123847579-123850676	IMR90	lung:	n/a	n/a
21	MXI1	chr12:123847099-123850811	SK-N-SH	brain:	n/a	n/a
22	MYC	chr12:123847766-123848515	MCF10A-Er-Src	breast:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
23	ELF1	chr12:123847840-123848477	MCF-7	breast:	n/a	chr12:123848160-123848169 chr12:123848158-123848171 chr12:123848159-123848170 chr12:123848159-123848170
24	MAX	chr12:123847669-123850598	A549	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
25	MYC	chr12:123847763-123850602	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
26	MAX	chr12:123847821-123848764	HepG2	liver:	n/a	chr12:123848142-123848149 chr12:123848144-123848151 chr12:123848138-123848153 chr12:123848140-123848155
27	HCFC1	chr12:123847639-123850810	Hela-S3	cervix:	n/a	n/a
28	SIN3AK20	chr12:123847813-123848631	PANC-1	pancreas:	n/a	n/a
29	NR2F2	chr12:123847823-123848537	MCF-7	breast:	n/a	chr12:123848103-123848118
30	POLR2A	chr12:123847692-123848942	GM12878	blood:	n/a	n/a
31	MXI1	chr12:123847776-123848875	Hela-S3	cervix:	n/a	n/a
32	ELF1	chr12:123847819-123848556	K562	blood:	n/a	chr12:123848160-123848169 chr12:123848158-123848171 chr12:123848159-123848170 chr12:123848159-123848170
33	POLR2A	chr12:123847838-123850743	H1-hESC	embryonic stem cell:	n/a	n/a
34	ZC3H11A	chr12:123847829-123847965	K562	blood:	n/a	n/a
35	SIN3AK20	chr12:123847702-123850572	MCF-7	breast:	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	chr12:123847748..123850760-chr12:123875045..123877875,5	MCF-7	breast:
5	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
6	chr12:123846880..123851536-chr12:123865445..123870876,12	MCF-7	breast:
7	chr12:123829057..123831002-chr12:123845125..123847852,2	K562	blood:
8	chr12:123846861..123850261-chr12:124066655..124071408,9	MCF-7	breast:
9	chr12:123847204..123849398-chr12:123874460..123876425,2	K562	blood:
10	chr12:123833002..123837136-chr12:123847313..123849620,3	MCF-7	breast:
11	chr12:123832815..123836496-chr12:123847723..123851604,4	MCF-7	breast:
12	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
13	chr12:123847713..123850022-chr12:124067528..124071055,3	MCF-7	breast:
14	chr12:123847169..123849970-chr12:124085128..124088523,3	K562	blood:
15	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:
16	chr12:123846000..123850093-chr12:124067189..124070124,4	K562	blood:
17	chr12:123753451..123758032-chr12:123846651..123850459,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256092	TF binding region
ENSG00000139697	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000185344	Chromatin interaction
ENSG00000207189	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000111358	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10846516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[AMR][1000 genomes]
rs11057167	1.00[AFR][1000 genomes]
rs11057171	1.00[AFR][1000 genomes]
rs11057173	1.00[AFR][1000 genomes]
rs11057182	1.00[AFR][1000 genomes]
rs11057186	1.00[AFR][1000 genomes]
rs11057195	1.00[AFR][1000 genomes]
rs11057199	1.00[AFR][1000 genomes]
rs11057213	1.00[AFR][1000 genomes]
rs11057215	1.00[AFR][1000 genomes]
rs11057239	1.00[CEU][hapmap]
rs11057252	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11057257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11057265	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs11057272	1.00[AMR][1000 genomes]
rs11057278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs11057281	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11057282	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12368208	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[AFR][1000 genomes]
rs12371718	1.00[AFR][1000 genomes]
rs12372699	1.00[AFR][1000 genomes]
rs28624763	0.88[EUR][1000 genomes]
rs28664930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs28690392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28698461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28828722	0.94[EUR][1000 genomes]
rs28836481	0.85[EUR][1000 genomes]
rs28875264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3881293	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55634633	1.00[AMR][1000 genomes]
rs55932027	1.00[EUR][1000 genomes]
rs56104963	1.00[AFR][1000 genomes]
rs73216930	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73216932	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73231941	1.00[AFR][1000 genomes]
rs73231994	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73233508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7486351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123832400-123848200	Weak transcription	Esophagus	oesophagus
2	chr12:123835000-123848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:123836000-123848200	Weak transcription	Gastric	stomach
4	chr12:123843000-123848000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr12:123845000-123848000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr12:123845600-123848000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:123847000-123848000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:123847000-123848000	Enhancers	Fetal Brain Male	brain
9	chr12:123847000-123848200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:123847000-123848800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:123847200-123848000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:123847200-123848000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:123847200-123848000	Enhancers	Left Ventricle	heart
14	chr12:123847200-123848200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:123847200-123848400	Flanking Active TSS	Dnd41	blood
16	chr12:123847200-123848600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:123847200-123850600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:123847400-123848000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:123847400-123848000	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:123847400-123848000	Enhancers	Fetal Heart	heart
21	chr12:123847400-123848000	Flanking Active TSS	A549	lung
22	chr12:123847400-123848200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr12:123847400-123848200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:123847400-123848200	Enhancers	Colonic Mucosa	Colon
25	chr12:123847400-123848200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr12:123847400-123848400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr12:123847400-123848400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr12:123847400-123848400	Weak transcription	Spleen	Spleen
29	chr12:123847400-123848400	Flanking Active TSS	Hela-S3	cervix
30	chr12:123847400-123848600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr12:123847400-123848600	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr12:123847400-123848800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr12:123847400-123848800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:123847400-123849000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr12:123847400-123850400	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr12:123847400-123850600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:123847400-123850600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:123847400-123850600	Active TSS	Right Ventricle	heart
39	chr12:123847400-123850800	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr12:123847600-123848000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr12:123847600-123848000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:123847600-123848000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:123847600-123848000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr12:123847600-123848000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:123847600-123848000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:123847600-123848000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr12:123847600-123848000	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr12:123847600-123848000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr12:123847600-123848000	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr12:123847600-123848000	Active TSS	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links