Variant report

Variant	rs3852588
Chromosome Location	chr12:120540532-120540533
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	RAD21	chr12:120540414-120540798	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr12:120540273-120540865	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr12:120540440-120540590	GM12868	blood:	n/a	n/a
4	SPI1	chr12:120540380-120540831	HL-60	blood:	n/a	chr12:120540598-120540607 chr12:120540596-120540609 chr12:120540597-120540610
5	SPI1	chr12:120540306-120540844	HL-60	blood:	n/a	chr12:120540598-120540607 chr12:120540596-120540609 chr12:120540597-120540610
6	CTCF	chr12:120540420-120540570	GM12874	blood:	n/a	n/a
7	POLR2A	chr12:120540079-120540542	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120539632..120542312-chr12:120549101..120550620,2	MCF-7	breast:
2	chr12:120534614..120537528-chr12:120540036..120541614,2	MCF-7	breast:
3	chr12:120537048..120541245-chr12:120553607..120557723,6	MCF-7	breast:
4	chr12:120539799..120542911-chr12:120545962..120548810,4	MCF-7	breast:
5	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
6	chr12:120538101..120541195-chr12:120726908..120731130,5	MCF-7	breast:
7	chr12:120539029..120543839-chr12:120726926..120732179,7	MCF-7	breast:
8	chr12:120538883..120540818-chr12:120636912..120639321,2	MCF-7	breast:
9	chr12:120536601..120538960-chr12:120539868..120542086,3	K562	blood:
10	chr12:120524045..120526996-chr12:120539011..120541039,3	MCF-7	breast:

Variant related genes	Relation type
RAB35	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000255857	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10744747	0.81[ASN][1000 genomes]
rs11064998	0.81[ASN][1000 genomes]
rs11065004	0.85[ASN][1000 genomes]
rs11065014	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065017	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065018	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12311327	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12320072	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2240311	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393570	0.85[ASN][1000 genomes]
rs3742044	0.80[ASN][1000 genomes]
rs3759399	0.94[ASN][1000 genomes]
rs3852586	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3886910	0.80[ASN][1000 genomes]
rs3999575	0.95[ASN][1000 genomes]
rs4105713	0.83[AMR][1000 genomes]
rs4351876	0.80[ASN][1000 genomes]
rs6490278	0.80[ASN][1000 genomes]
rs6490281	0.81[AMR][1000 genomes]
rs6490283	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6490284	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7295717	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7302874	0.80[ASN][1000 genomes]
rs7305625	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7306739	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7312811	0.81[ASN][1000 genomes]
rs7314959	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956436	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7960725	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7961738	0.80[ASN][1000 genomes]
rs7962812	0.81[ASN][1000 genomes]
rs7971249	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977281	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv560434	chr12:120534147-120545718	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:120525800-120553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:120527400-120546800	Strong transcription	Thymus	Thymus
4	chr12:120527600-120546000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:120529000-120546800	Strong transcription	Dnd41	blood
6	chr12:120529600-120543000	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:120529800-120542200	Strong transcription	Fetal Intestine Large	intestine
8	chr12:120532800-120541600	Weak transcription	K562	blood
9	chr12:120533600-120542800	Strong transcription	A549	lung
10	chr12:120533800-120553000	Weak transcription	Fetal Kidney	kidney
11	chr12:120534200-120542800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:120534200-120542800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:120534200-120542800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:120534400-120553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:120534600-120546800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:120534600-120547200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:120534600-120548200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:120536000-120541800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:120536200-120543000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:120536800-120540800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:120536800-120541200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:120536800-120541800	Genic enhancers	Esophagus	oesophagus
23	chr12:120537000-120540800	Genic enhancers	Right Ventricle	heart
24	chr12:120537000-120540800	Weak transcription	Hela-S3	cervix
25	chr12:120537000-120543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:120537200-120541000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:120537200-120541000	Weak transcription	Osteobl	bone
28	chr12:120537400-120541600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:120537400-120541600	Genic enhancers	Gastric	stomach
30	chr12:120537400-120542400	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr12:120537400-120542600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:120537600-120540800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:120537600-120541400	Genic enhancers	Fetal Muscle Leg	muscle
34	chr12:120537600-120541600	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr12:120537800-120541000	Enhancers	Left Ventricle	heart
36	chr12:120537800-120543400	Genic enhancers	Spleen	Spleen
37	chr12:120537800-120544400	Genic enhancers	Placenta	Placenta
38	chr12:120538000-120540600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
39	chr12:120538000-120540800	Enhancers	Right Atrium	heart
40	chr12:120538000-120541000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:120538000-120541000	Genic enhancers	Duodenum Mucosa	Duodenum
42	chr12:120538200-120540600	Enhancers	Psoas Muscle	Psoas
43	chr12:120538200-120541200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:120538200-120543000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:120538400-120540600	Genic enhancers	Fetal Thymus	thymus
46	chr12:120538400-120540800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:120538400-120541000	Genic enhancers	Placenta Amnion	Placenta Amnion
48	chr12:120538400-120541200	Genic enhancers	Lung	lung
49	chr12:120538400-120541400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr12:120538600-120540600	Weak transcription	HepG2	liver

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