Variant report

Variant	rs3852586
Chromosome Location	chr12:120524687-120524688
allele	C/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	chr12:120524592-120525147	HUVEC	blood vessel:	n/a	n/a
2	SIN3AK20	chr12:120524545-120525255	PANC-1	pancreas:	n/a	n/a
3	RCOR1	chr12:120524652-120525404	GM12878	blood:	n/a	n/a
4	EP300	chr12:120524603-120525293	T-47D	breast:	n/a	chr12:120524775-120524791 chr12:120525073-120525089
5	MYC	chr12:120524614-120525499	NB4	blood:	n/a	chr12:120525082-120525092 chr12:120524949-120524958 chr12:120524693-120524703 chr12:120524726-120524736 chr12:120524693-120524702
6	POLR2A	chr12:120524542-120525074	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:120524627-120525491	Hela-S3	cervix:	n/a	n/a
8	USF1	chr12:120524640-120525409	ECC-1	luminal epithelium:	n/a	chr12:120524860-120524876 chr12:120524852-120524868
9	POLR2A	chr12:120524620-120525288	A549	lung:	n/a	n/a
10	NFIC	chr12:120524499-120525476	ECC-1	luminal epithelium:	n/a	chr12:120524984-120525000 chr12:120524983-120525000 chr12:120524982-120525010
11	USF1	chr12:120524576-120525215	A549	lung:	n/a	chr12:120524860-120524876 chr12:120524852-120524868
12	RAD21	chr12:120524529-120525366	Hela-S3	cervix:	n/a	chr12:120525323-120525336 chr12:120524862-120524874 chr12:120524688-120524702 chr12:120524860-120524879 chr12:120525324-120525338
13	GABPA	chr12:120524604-120525370	H1-hESC	embryonic stem cell:	n/a	chr12:120525082-120525091
14	NFATC1	chr12:120524667-120525309	GM12878	blood:	n/a	n/a
15	REST	chr12:120524679-120525015	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr12:120524641-120524963	A549	lung:	n/a	n/a
17	MAX	chr12:120524594-120525415	H1-hESC	embryonic stem cell:	n/a	chr12:120525082-120525092 chr12:120524949-120524958 chr12:120524693-120524703 chr12:120524726-120524736 chr12:120524693-120524702
18	TAF7	chr12:120524609-120525080	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOXA1	chr12:120524674-120525264	T-47D	breast:	n/a	n/a
20	SIN3A	chr12:120524668-120525409	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:120524582-120525426	ECC-1	luminal epithelium:	n/a	n/a
22	TEAD4	chr12:120524550-120525323	A549	lung:	n/a	chr12:120524836-120524845
23	SIN3AK20	chr12:120524426-120525656	MCF-7	breast:	n/a	n/a
24	RUNX3	chr12:120524629-120525558	GM12878	blood:	n/a	chr12:120525285-120525302
25	POLR2A	chr12:120524641-120525419	MCF-7	breast:	n/a	n/a
26	FOS	chr12:120524461-120525252	MCF10A-Er-Src	breast:	n/a	chr12:120525179-120525189 chr12:120525179-120525189
27	POLR2A	chr12:120524365-120525609	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr12:120524619-120525207	SK-N-SH	brain:	n/a	n/a
29	SIN3AK20	chr12:120524493-120525502	MCF-7	breast:	n/a	n/a
30	TBL1XR1	chr12:120524675-120525122	K562	blood:	n/a	n/a
31	CTCF	chr12:120524391-120525597	SK-N-SH	brain:	n/a	chr12:120524862-120524880 chr12:120524864-120524877 chr12:120524864-120524877 chr12:120525324-120525337 chr12:120524863-120524879
32	MAFK	chr12:120524613-120525147	Hela-S3	cervix:	n/a	chr12:120524826-120524842 chr12:120524830-120524841 chr12:120524826-120524841 chr12:120524831-120524842 chr12:120524829-120524843 chr12:120524831-120524842
33	MXI1	chr12:120524651-120525144	K562	blood:	n/a	chr12:120524943-120524958
34	TAF1	chr12:120524527-120525036	A549	lung:	n/a	n/a
35	RAD21	chr12:120524661-120524994	GM12878	blood:	n/a	chr12:120524862-120524874 chr12:120524688-120524702 chr12:120524860-120524879
36	POLR2A	chr12:120524574-120525163	K562	blood:	n/a	n/a
37	ETS1	chr12:120524571-120525165	A549	lung:	n/a	chr12:120524883-120524894
38	REST	chr12:120524609-120525084	PFSK-1	brain:	n/a	n/a
39	CTBP2	chr12:120524645-120525209	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:120524667-120525394	Raji	blood:	n/a	n/a
41	RCOR1	chr12:120524425-120525756	IMR90	lung:	n/a	n/a
42	RAD21	chr12:120524644-120525169	SK-N-SH_RA	brain:	n/a	chr12:120524862-120524874 chr12:120524688-120524702 chr12:120524860-120524879
43	BACH1	chr12:120524371-120525190	H1-hESC	embryonic stem cell:	n/a	n/a
44	CREB1	chr12:120524656-120525283	ECC-1	luminal epithelium:	n/a	n/a
45	CREB1	chr12:120524597-120525369	K562	blood:	n/a	n/a
46	POLR2A	chr12:120524572-120525186	PANC-1	pancreas:	n/a	n/a
47	ETS1	chr12:120524620-120525169	K562	blood:	n/a	chr12:120524883-120524894
48	POLR2A	chr12:120524637-120525253	GM15510	blood:	n/a	n/a
49	POU2F2	chr12:120524619-120525247	GM12891	blood:	n/a	n/a
50	E2F6	chr12:120524669-120524997	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:120524653-120524703	GM12892	blood:	n/a
2	chr12:120524653-120524703	K562	blood:	n/a
3	chr12:120524653-120524703	AG04450	lung:	fetal
4	chr12:120524653-120524703	NT2-D1	testis:	n/a
5	chr12:120524653-120524703	AG09319	gingival:	n/a
6	chr12:120524653-120524703	HCM	heart:	n/a
7	chr12:120524653-120524703	NB4	blood:	n/a
8	chr12:120524653-120524703	HepG2	liver:	n/a
9	chr12:120524653-120524703	HEK293	kidney:	embryo
10	chr12:120524653-120524703	T-47D	breast:	n/a
11	chr12:120524653-120524703	PrEC	prostate:	n/a
12	chr12:120524653-120524703	MCF-7	breast:	n/a
13	chr12:120524653-120524703	HEEpiC	esophagus:	n/a
14	chr12:120524653-120524703	A549	lung:	n/a
15	chr12:120524653-120524703	HRE	kidney:	n/a
16	chr12:120524653-120524703	HL-60	blood:	n/a
17	chr12:120524653-120524703	BJ	skin:	n/a
18	chr12:120524653-120524703	SKMC	muscle:	n/a
19	chr12:120524653-120524703	H1-hESC	embryonic stem cell:	embryo
20	chr12:120524653-120524703	HRPEpiC	eye:	n/a
21	chr12:120524653-120524703	SK-N-SH_RA	brain:	n/a
22	chr12:120524653-120524703	HAEpiC	amniotic membrane:	n/a
23	chr12:120524653-120524703	PANC-1	pancreas:	n/a
24	chr12:120524653-120524703	GM06990	blood:	n/a
25	chr12:120524653-120524703	GM12891	blood:	n/a
26	chr12:120524653-120524703	GM12878	blood:	n/a
27	chr12:120524653-120524703	BE2_C	brain:	n/a
28	chr12:120524653-120524703	ECC-1	luminal epithelium:	n/a
29	chr12:120524653-120524703	HRCEpiC	kidney:	n/a
30	chr12:120524653-120524703	HNPCEpiC	eye:	n/a
31	chr12:120524653-120524703	SAEC	small airway:	n/a
32	chr12:120524653-120524703	SK-N-MC	brain:	n/a
33	chr12:120524653-120524703	CMK	blood:	n/a
34	chr12:120524653-120524703	NH-A	brain:	n/a
35	chr12:120524653-120524703	Caco-2	colon:	n/a
36	chr12:120524653-120524703	GM19239	blood:	n/a
37	chr12:120524653-120524703	ovcar-3	ovarian:	n/a
38	chr12:120524653-120524703	Jurkat	blood:	n/a
39	chr12:120524653-120524703	LNCaP	prostate:	n/a
40	chr12:120524653-120524703	AoSMC	blood vessel:	n/a
41	chr12:120524653-120524703	Hepatocyte	liver:	n/a
42	chr12:120524653-120524703	SK-N-SH	brain:	n/a
43	chr12:120524653-120524703	NHDF-neo	bronchial:	n/a
44	chr12:120524653-120524703	MCF10A-Er-Src	breast:	n/a
45	chr12:120524653-120524703	HMEC	breast:	n/a
46	chr12:120524653-120524703	ProgFib	skin:	n/a
47	chr12:120524653-120524703	HCF	heart:	n/a
48	chr12:120524653-120524703	PFSK-1	brain:	n/a
49	chr12:120524653-120524703	AG04449	skin:	fetal
50	chr12:120524653-120524703	AG10803	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120426492..120427432-chr12:120524501..120525382,2	K562	blood:
2	chr12:120523806..120527797-chr12:120636547..120640278,4	K562	blood:
3	chr12:120522807..120526781-chr12:120552984..120555977,5	MCF-7	breast:
4	chr12:120463438..120466010-chr12:120520839..120524838,3	K562	blood:
5	chr12:120426345..120430179-chr12:120522366..120526124,6	MCF-7	breast:
6	chr12:120523464..120525558-chr12:120724032..120726437,2	MCF-7	breast:
7	chr12:120502289..120504237-chr12:120523467..120526114,3	MCF-7	breast:
8	chr12:120432888..120433671-chr12:120524512..120525195,2	MCF-7	breast:
9	chr12:120425138..120431100-chr12:120522252..120526480,6	MCF-7	breast:
10	chr12:120104543..120107131-chr12:120523519..120526303,2	K562	blood:
11	chr12:120522735..120525949-chr12:120728856..120731455,3	MCF-7	breast:
12	chr12:120516392..120519629-chr12:120522299..120526029,10	MCF-7	breast:
13	chr12:120500713..120503660-chr12:120523490..120525238,2	MCF-7	breast:
14	chr12:120523567..120526136-chr12:120728252..120731056,2	MCF-7	breast:
15	chr12:120523103..120525507-chr12:120553148..120557621,6	MCF-7	breast:
16	chr12:120524045..120526996-chr12:120539011..120541039,3	MCF-7	breast:

Variant related genes	Relation type
CCDC64	TF binding region
CCDC64	CpG island
ENSG00000248636	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000111725	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10744747	0.83[ASN][1000 genomes]
rs11064986	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11064998	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065004	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065014	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065017	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065018	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12311327	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12320072	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239200	0.83[CHB][hapmap]
rs2239201	0.83[CHB][hapmap]
rs2240311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393570	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2893812	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs3742044	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3759399	0.97[ASN][1000 genomes]
rs3852588	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3886910	0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3999575	0.98[ASN][1000 genomes]
rs4105713	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4351876	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4767870	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs4767873	0.82[ASN][1000 genomes]
rs6490278	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6490280	0.82[EUR][1000 genomes]
rs6490281	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6490283	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6490284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295717	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7300023	0.82[CHB][hapmap]
rs7302874	0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7304325	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7305625	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7306739	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312811	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314959	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7956436	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7960725	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7961738	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7962812	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7965829	0.83[CHB][hapmap]
rs7971249	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7977281	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120502600-120525200	Weak transcription	Spleen	Spleen
2	chr12:120518200-120528600	Weak transcription	Gastric	stomach
3	chr12:120518600-120525200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:120523000-120525000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:120523800-120525600	Enhancers	Stomach Mucosa	stomach
6	chr12:120524000-120524800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr12:120524000-120524800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:120524000-120524800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr12:120524000-120524800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:120524200-120525000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:120524200-120525200	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr12:120524200-120525200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:120524200-120525400	Enhancers	Fetal Brain Male	brain
14	chr12:120524400-120524800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:120524400-120524800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:120524400-120524800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr12:120524400-120524800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr12:120524400-120524800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:120524400-120524800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:120524400-120524800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr12:120524400-120524800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr12:120524400-120524800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr12:120524400-120524800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:120524400-120524800	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr12:120524400-120524800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr12:120524400-120524800	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr12:120524400-120524800	Flanking Active TSS	HepG2	liver
28	chr12:120524400-120524800	Flanking Active TSS	K562	blood
29	chr12:120524400-120524800	Flanking Active TSS	NH-A	brain
30	chr12:120524400-120524800	Flanking Active TSS	NHEK	skin
31	chr12:120524400-120524800	Flanking Active TSS	Osteobl	bone
32	chr12:120524400-120525000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr12:120524400-120525200	Enhancers	Primary B cells from cord blood	blood
34	chr12:120524400-120525200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:120524400-120525200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:120524400-120525200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:120524400-120525200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:120524400-120525400	Active TSS	Brain Substantia Nigra	brain
39	chr12:120524400-120525400	Active TSS	HSMMtube	muscle
40	chr12:120524400-120525600	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr12:120524400-120525600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr12:120524400-120525600	Flanking Active TSS	Dnd41	blood
43	chr12:120524400-120525600	Flanking Active TSS	Hela-S3	cervix
44	chr12:120524400-120525800	Enhancers	Fetal Heart	heart
45	chr12:120524600-120524800	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr12:120524600-120524800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
47	chr12:120524600-120524800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:120524600-120524800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:120524600-120524800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:120524600-120524800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links