Variant report

Variant	rs7487602
Chromosome Location	chr12:48214833-48214834
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	MYC	chr12:48213653-48215083	Hela-S3	cervix:	n/a	chr12:48213792-48213802
2	PBX3	chr12:48213512-48214863	SK-N-SH	brain:	n/a	n/a
3	NR3C1	chr12:48212927-48214894	A549	lung:	n/a	chr12:48214341-48214348 chr12:48214168-48214181
4	TAF1	chr12:48212590-48215151	ECC-1	luminal epithelium:	n/a	n/a
5	RAD21	chr12:48213608-48215016	ECC-1	luminal epithelium:	n/a	n/a
6	ESR1	chr12:48214307-48214969	ECC-1	luminal epithelium:	n/a	n/a
7	GATA3	chr12:48213426-48214878	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr12:48212665-48215399	Hela-S3	cervix:	n/a	n/a
9	ATF3	chr12:48214245-48214840	A549	lung:	n/a	n/a
10	TFAP2A	chr12:48212376-48215217	Hela-S3	cervix:	n/a	chr12:48213280-48213288 chr12:48212492-48212502 chr12:48215068-48215078 chr12:48212492-48212502 chr12:48213646-48213656 chr12:48212848-48212858 chr12:48213279-48213287 chr12:48212809-48212821 chr12:48213280-48213288 chr12:48215066-48215080 chr12:48213278-48213289 chr12:48213280-48213288 chr12:48212846-48212860 chr12:48213278-48213289 chr12:48212492-48212502 chr12:48215066-48215080 chr12:48212687-48212699 chr12:48213279-48213287 chr12:48213278-48213289 chr12:48212843-48212858 chr12:48212492-48212502 chr12:48213279-48213287 chr12:48212687-48212698 chr12:48212848-48212860 chr12:48213646-48213656 chr12:48213278-48213289
11	TCF12	chr12:48212677-48215465	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr12:48213743-48214876	A549	lung:	n/a	chr12:48213792-48213802
13	MAZ	chr12:48212023-48214870	K562	blood:	n/a	chr12:48213219-48213228 chr12:48213792-48213802
14	GATA3	chr12:48213586-48215164	MCF-7	breast:	n/a	n/a
15	NFIC	chr12:48213441-48215549	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr12:48213532-48215230	A549	lung:	n/a	chr12:48213792-48213802
17	ATF3	chr12:48213924-48214846	A549	lung:	n/a	n/a
18	ESR1	chr12:48214260-48214996	ECC-1	luminal epithelium:	n/a	n/a
19	REST	chr12:48214171-48214855	PFSK-1	brain:	n/a	chr12:48214741-48214761
20	JUND	chr12:48214128-48214964	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr12:48212964-48214913	MCF-7	breast:	n/a	n/a
22	JUND	chr12:48213496-48215444	SK-N-SH	brain:	n/a	chr12:48215305-48215315 chr12:48214984-48214993
23	SP1	chr12:48213548-48215043	A549	lung:	n/a	chr12:48213779-48213793 chr12:48213788-48213802 chr12:48213700-48213712 chr12:48213784-48213798 chr12:48214300-48214314 chr12:48213782-48213794 chr12:48213783-48213792
24	MAX	chr12:48213591-48215538	ECC-1	luminal epithelium:	n/a	chr12:48213792-48213802
25	JUND	chr12:48214117-48214871	SK-N-SH	brain:	n/a	n/a
26	FOSL2	chr12:48214222-48214899	MCF-7	breast:	n/a	n/a
27	FOXM1	chr12:48213621-48215061	ECC-1	luminal epithelium:	n/a	n/a
28	MAFK	chr12:48213915-48214858	Hela-S3	cervix:	n/a	n/a
29	GATA3	chr12:48213491-48214956	T-47D	breast:	n/a	n/a
30	POLR2A	chr12:48212148-48215367	H1-hESC	embryonic stem cell:	n/a	n/a
31	RCOR1	chr12:48213615-48215410	IMR90	lung:	n/a	n/a
32	SP1	chr12:48214260-48214872	H1-hESC	embryonic stem cell:	n/a	chr12:48214300-48214314
33	POLR2A	chr12:48213539-48214852	MCF-7	breast:	n/a	n/a
34	NR2F2	chr12:48214238-48215180	MCF-7	breast:	n/a	n/a
35	POLR2A	chr12:48214467-48214848	A549	lung:	n/a	n/a
36	PBX3	chr12:48213564-48214945	A549	lung:	n/a	n/a
37	ELK1	chr12:48213838-48215147	Hela-S3	cervix:	n/a	n/a
38	REST	chr12:48213869-48214910	A549	lung:	n/a	chr12:48214741-48214761
39	TAF1	chr12:48213566-48214883	A549	lung:	n/a	n/a
40	MAX	chr12:48213553-48215530	ECC-1	luminal epithelium:	n/a	chr12:48213792-48213802
41	POLR2A	chr12:48212564-48215383	Hela-S3	cervix:	n/a	n/a
42	TCF12	chr12:48213538-48215303	A549	lung:	n/a	n/a
43	POLR2A	chr12:48214397-48215137	H1-hESC	embryonic stem cell:	n/a	n/a
44	TEAD4	chr12:48214202-48214916	SK-N-SH	brain:	n/a	n/a
45	FOXM1	chr12:48213479-48215252	ECC-1	luminal epithelium:	n/a	n/a
46	ELK4	chr12:48214014-48214851	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr12:48213393-48214948	U87	brain:	n/a	n/a
48	POLR2A	chr12:48210923-48215326	Raji	blood:	n/a	n/a
49	NFIC	chr12:48214452-48214886	HepG2	liver:	n/a	n/a
50	POLR2A	chr12:48214434-48214909	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48184371..48186432-chr12:48213381..48215555,2	MCF-7	breast:
2	chr12:48214779..48215373-chr12:48231061..48231841,2	MCF-7	breast:
3	chr12:48180097..48182896-chr12:48212671..48214919,5	MCF-7	breast:
4	chr12:48118580..48122371-chr12:48212442..48215354,3	MCF-7	breast:
5	chr12:48166096..48168794-chr12:48212793..48215345,3	K562	blood:
6	chr12:48144391..48147829-chr12:48212557..48216683,4	MCF-7	breast:
7	chr12:48141723..48143940-chr12:48213579..48216155,2	MCF-7	breast:
8	chr12:48214550..48215216-chr12:48232260..48232928,2	K562	blood:
9	chr12:48214165..48215059-chr3:14219720..14220575,2	Hela-S3	cervix:
10	chr12:48214570..48215265-chrX:73834061..73834603,2	Hela-S3	cervix:
11	chr12:48214553..48215217-chr4:71704540..71705239,2	Hela-S3	cervix:
12	chr12:48098678..48101690-chr12:48212441..48216325,5	MCF-7	breast:
13	chr12:48170860..48172762-chr12:48213398..48215365,3	MCF-7	breast:
14	chr12:6643615..6644394-chr12:48214539..48215281,2	Hela-S3	cervix:
15	chr12:48166096..48168794-chr12:48212793..48215345,4	K562	blood:
16	chr12:48212981..48215317-chr3:161089373..161090906,2	MCF-7	breast:
17	chr12:48213554..48216263-chr17:57923656..57925341,2	MCF-7	breast:
18	chr12:48214604..48217518-chr12:48297846..48300533,2	MCF-7	breast:
19	chr12:48214051..48215050-chr16:88729320..88730007,2	Hela-S3	cervix:
20	chr12:48214340..48214979-chr12:115121754..115122514,2	Hela-S3	cervix:
21	chr12:48171729..48173429-chr12:48213188..48215174,2	K562	blood:

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000005175	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000131263	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000167508	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000111405	Chromatin interaction
ENSG00000132463	Chromatin interaction
ENSG00000111640	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000260630	Chromatin interaction
ENSG00000154767	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000170860	Chromatin interaction
ENSG00000135111	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11168256	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168257	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168258	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574052	1.00[ASN][1000 genomes]
rs12721362	0.81[AMR][1000 genomes]
rs17721101	1.00[ASN][1000 genomes]
rs55713656	1.00[ASN][1000 genomes]
rs55913294	0.83[AMR][1000 genomes]
rs73109811	1.00[ASN][1000 genomes]
rs7487637	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973956	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer 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	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription 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	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	esv3404223	chr12:48212210-48215058	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	50 gene(s)	inside rSNPs	n/a
12	esv3357843	chr12:48212735-48214833	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	50 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48213000-48215000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:48213800-48215400	Flanking Active TSS	Colonic Mucosa	Colon
3	chr12:48214000-48215000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:48214000-48215000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr12:48214000-48215000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:48214000-48215000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:48214000-48215000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:48214000-48215000	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr12:48214000-48215000	Flanking Active TSS	Fetal Muscle Trunk	muscle
10	chr12:48214000-48215000	Flanking Active TSS	Fetal Muscle Leg	muscle
11	chr12:48214000-48215000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr12:48214000-48215200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:48214000-48215200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr12:48214000-48215200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:48214000-48215200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:48214000-48215200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr12:48214000-48215200	Flanking Active TSS	Placenta	Placenta
18	chr12:48214000-48215200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr12:48214000-48215200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr12:48214000-48215400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr12:48214000-48215400	Flanking Active TSS	Hela-S3	cervix
22	chr12:48214200-48215000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:48214200-48215000	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr12:48214200-48215200	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr12:48214200-48215200	Flanking Active TSS	Thymus	Thymus
26	chr12:48214200-48215400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:48214200-48215800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:48214200-48216400	Enhancers	Spleen	Spleen
29	chr12:48214400-48215000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:48214400-48215000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr12:48214400-48215000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:48214400-48215000	Enhancers	Primary B cells from peripheral blood	blood
33	chr12:48214400-48215000	Enhancers	Fetal Brain Male	brain
34	chr12:48214400-48215200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:48214400-48215200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:48214400-48215200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:48214400-48215200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:48214400-48215200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:48214400-48215200	Flanking Active TSS	NHEK	skin
40	chr12:48214400-48215400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:48214400-48215400	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr12:48214400-48216000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:48214400-48216000	Enhancers	Liver	Liver
44	chr12:48214400-48216000	Enhancers	Small Intestine	intestine
45	chr12:48214400-48216200	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr12:48214400-48216800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:48214400-48216800	Enhancers	Gastric	stomach
48	chr12:48214400-48217200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:48214400-48221400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:48214400-48226400	Enhancers	Primary T cells fromperipheralblood	blood

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