Variant report

Variant	rs2239760
Chromosome Location	chr12:121163518-121163519
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	RAD21	chr12:121163372-121163921	H1-hESC	embryonic stem cell:	n/a	chr12:121163546-121163556
2	POLR2A	chr12:121163400-121163903	ProgFib	skin:	n/a	n/a
3	POLR2A	chr12:121163490-121163888	GM10847	blood:	n/a	n/a
4	POLR2A	chr12:121163342-121164040	K562	blood:	n/a	n/a
5	IRF1	chr12:121163342-121163870	K562	blood:	n/a	chr12:121163611-121163625 chr12:121163540-121163554
6	PML	chr12:121163350-121164006	GM12878	blood:	n/a	n/a
7	SIN3A	chr12:121163015-121164112	H1-hESC	embryonic stem cell:	n/a	n/a
8	ARID3A	chr12:121163478-121163589	HepG2	liver:	n/a	n/a
9	ZKSCAN1	chr12:121163435-121163717	Hela-S3	cervix:	n/a	n/a
10	YY1	chr12:121163479-121163928	GM12878	blood:	n/a	chr12:121163544-121163553 chr12:121163542-121163556
11	NFATC1	chr12:121163137-121163631	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:121163455-121163899	GM15510	blood:	n/a	n/a
13	YY1	chr12:121163516-121163868	SK-N-SH_RA	brain:	n/a	chr12:121163544-121163553 chr12:121163542-121163556
14	MAX	chr12:121163389-121163861	Hela-S3	cervix:	n/a	n/a
15	PAX5	chr12:121163296-121163857	GM12878	blood:	n/a	chr12:121163571-121163590 chr12:121163640-121163649
16	MAX	chr12:121163437-121163865	H1-hESC	embryonic stem cell:	n/a	n/a
17	NFATC1	chr12:121163241-121163769	GM12878	blood:	n/a	n/a
18	MYC	chr12:121163352-121164090	K562	blood:	n/a	n/a
19	PAX5	chr12:121163419-121163952	GM12892	blood:	n/a	chr12:121163571-121163590 chr12:121163640-121163649
20	POLR2A	chr12:121163285-121163864	HepG2	liver:	n/a	n/a
21	RCOR1	chr12:121163423-121163771	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr12:121163415-121163825	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr12:121162579-121164122	ECC-1	luminal epithelium:	n/a	n/a
24	TCF12	chr12:121163257-121164388	A549	lung:	n/a	chr12:121163479-121163486
25	BRCA1	chr12:121163441-121163662	Hela-S3	cervix:	n/a	n/a
26	TAF1	chr12:121163427-121163878	GM12878	blood:	n/a	n/a
27	KAP1	chr12:121162964-121163852	U2OS	brain:	n/a	n/a
28	SP1	chr12:121163279-121163996	A549	lung:	n/a	chr12:121163614-121163623 chr12:121163544-121163553 chr12:121163543-121163552 chr12:121163614-121163628 chr12:121163542-121163554 chr12:121163613-121163625 chr12:121163543-121163553 chr12:121163615-121163624 chr12:121163543-121163552 chr12:121163542-121163554 chr12:121163542-121163553 chr12:121163543-121163557 chr12:121163543-121163553 chr12:121163613-121163625 chr12:121163613-121163624
29	NRF1	chr12:121163279-121163524	H1-hESC	embryonic stem cell:	n/a	chr12:121163492-121163501 chr12:121163491-121163502
30	POLR2A	chr12:121163454-121163878	Hela-S3	cervix:	n/a	n/a
31	SIN3A	chr12:121163392-121163583	GM12878	blood:	n/a	n/a
32	NRF1	chr12:121163344-121163673	GM12878	blood:	n/a	chr12:121163544-121163553 chr12:121163492-121163501 chr12:121163491-121163502
33	MAFK	chr12:121163370-121163673	Hela-S3	cervix:	n/a	n/a
34	E2F6	chr12:121163399-121163831	K562	blood:	n/a	chr12:121163544-121163553
35	POLR2A	chr12:121163320-121164044	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr12:121163276-121163846	HepG2	liver:	n/a	n/a
37	JUND	chr12:121163370-121163802	K562	blood:	n/a	chr12:121163616-121163625
38	TCF3	chr12:121163453-121163853	GM12878	blood:	n/a	n/a
39	MAZ	chr12:121163413-121163740	HepG2	liver:	n/a	n/a
40	PML	chr12:121163479-121163895	K562	blood:	n/a	n/a
41	CCNT2	chr12:121163407-121163971	K562	blood:	n/a	chr12:121163544-121163553 chr12:121163933-121163942
42	MAX	chr12:121163327-121164168	HepG2	liver:	n/a	n/a
43	YY1	chr12:121163406-121164097	GM12878	blood:	n/a	chr12:121163544-121163553 chr12:121163542-121163556
44	TAF1	chr12:121163269-121163909	H1-hESC	embryonic stem cell:	n/a	n/a
45	SMC3	chr12:121163474-121163899	Hela-S3	cervix:	n/a	chr12:121163546-121163556 chr12:121163783-121163793
46	HEY1	chr12:121163315-121163905	HepG2	liver:	n/a	n/a
47	POLR2A	chr12:121163334-121163995	GM12892	blood:	n/a	n/a
48	FOXP2	chr12:121163458-121163839	SK-N-MC	brain:	n/a	n/a
49	FOXP2	chr12:121163409-121163818	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr12:121163448-121163925	GM19193	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:121163497-121163547	ovcar-3	ovarian:	n/a
2	chr12:121163489-121163539	A549	lung:	n/a
3	chr12:121163489-121163539	HCM	heart:	n/a
4	chr12:121163497-121163547	HNPCEpiC	eye:	n/a
5	chr12:121163493-121163543	HPAEpiC	pulmonary alveolar:	n/a
6	chr12:121163493-121163543	U87	brain:	n/a
7	chr12:121163497-121163547	CMK	blood:	n/a
8	chr12:121163493-121163543	HL-60	blood:	n/a
9	chr12:121163497-121163547	HAEpiC	amniotic membrane:	n/a
10	chr12:121163497-121163547	PANC-1	pancreas:	n/a
11	chr12:121163489-121163539	BE2_C	brain:	n/a
12	chr12:121163497-121163547	GM19239	blood:	n/a
13	chr12:121163489-121163539	HL-60	blood:	n/a
14	chr12:121163489-121163539	NHBE	bronchial:	n/a
15	chr12:121163493-121163543	RPTEC	kidney:	n/a
16	chr12:121163497-121163547	BE2_C	brain:	n/a
17	chr12:121163493-121163543	GM06990	blood:	n/a
18	chr12:121163497-121163547	PFSK-1	brain:	n/a
19	chr12:121163497-121163547	MCF10A-Er-Src	breast:	n/a
20	chr12:121163497-121163547	HCT-116	colon:	n/a
21	chr12:121163493-121163543	HCT-116	colon:	n/a
22	chr12:121163497-121163547	HCPEpiC	choroid plexus:	n/a
23	chr12:121163493-121163543	ovcar-3	ovarian:	n/a
24	chr12:121163493-121163543	AG09309	skin:	n/a
25	chr12:121163493-121163543	T-47D	breast:	n/a
26	chr12:121163489-121163539	PrEC	prostate:	n/a
27	chr12:121163493-121163543	GM12891	blood:	n/a
28	chr12:121163493-121163543	PFSK-1	brain:	n/a
29	chr12:121163497-121163547	NH-A	brain:	n/a
30	chr12:121163493-121163543	ECC-1	luminal epithelium:	n/a
31	chr12:121163497-121163547	NB4	blood:	n/a
32	chr12:121163493-121163543	HCPEpiC	choroid plexus:	n/a
33	chr12:121163489-121163539	ProgFib	skin:	n/a
34	chr12:121163497-121163547	HCM	heart:	n/a
35	chr12:121163493-121163543	HCF	heart:	n/a
36	chr12:121163489-121163539	BJ	skin:	n/a
37	chr12:121163497-121163547	SK-N-SH	brain:	n/a
38	chr12:121163489-121163539	AG04450	lung:	fetal
39	chr12:121163489-121163539	SK-N-SH	brain:	n/a
40	chr12:121163497-121163547	Hela-S3	cervix:	n/a
41	chr12:121163497-121163547	NHDF-neo	bronchial:	n/a
42	chr12:121163497-121163547	NT2-D1	testis:	n/a
43	chr12:121163489-121163539	AG09309	skin:	n/a
44	chr12:121163497-121163547	ECC-1	luminal epithelium:	n/a
45	chr12:121163497-121163547	HRCEpiC	kidney:	n/a
46	chr12:121163497-121163547	Jurkat	blood:	n/a
47	chr12:121163493-121163543	NT2-D1	testis:	n/a
48	chr12:121163489-121163539	K562	blood:	n/a
49	chr12:121163489-121163539	GM19239	blood:	n/a
50	chr12:121163497-121163547	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121018631..121020878-chr12:121162530..121164769,2	MCF-7	breast:
2	chr12:121163485..121165709-chr12:121272071..121274503,2	MCF-7	breast:
3	chr12:121124457..121126009-chr12:121161896..121164295,2	K562	blood:
4	chr12:121136675..121138856-chr12:121162469..121164078,2	K562	blood:
5	chr12:121148319..121151196-chr12:121161623..121163655,2	K562	blood:
6	chr12:121146305..121152610-chr12:121160959..121168394,8	MCF-7	breast:
7	chr12:120729060..120730758-chr12:121163308..121164812,2	K562	blood:
8	chr12:121163197..121163956-chr16:31191423..31192105,2	Hela-S3	cervix:
9	chr12:121124509..121126833-chr12:121162138..121164295,2	K562	blood:

Variant related genes	Relation type
ACADS	TF binding region
ENSG00000256569	TF binding region
ENSG00000256569	CpG island
ACADS	CpG island
ENSG00000175970	Chromatin interaction
ENSG00000167272	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000256364	Chromatin interaction
ENSG00000157837	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10431384	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs10431385	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10431386	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs10849778	0.89[YRI][hapmap]
rs10849781	0.80[CHD][hapmap]
rs11065223	0.82[EUR][1000 genomes]
rs17847	0.82[EUR][1000 genomes]
rs1814851	0.80[EUR][1000 genomes]
rs2005455	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393778	0.90[ASN][1000 genomes]
rs2948149	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021338	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34734847	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35360964	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3751166	0.81[CHD][hapmap]
rs3752531	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3829290	0.81[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs3914	0.85[CEU][hapmap]
rs3915	0.80[EUR][1000 genomes]
rs548093	0.85[EUR][1000 genomes]
rs555404	0.82[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs556001	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs55730005	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56273049	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs575437	0.82[EUR][1000 genomes]
rs6490300	0.80[EUR][1000 genomes]
rs658521	0.82[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs695948	0.85[EUR][1000 genomes]
rs695949	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs695952	0.82[EUR][1000 genomes]
rs696337	0.82[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs696339	0.81[EUR][1000 genomes]
rs697854	0.81[EUR][1000 genomes]
rs708783	0.82[EUR][1000 genomes]
rs7308648	0.82[EUR][1000 genomes]
rs7973568	0.81[CHD][hapmap]
rs7976497	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs998727	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv899558	chr12:121161589-121179939	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2239760	MED13L	cis	parietal	SCAN
rs2239760	UNC119B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121151400-121163600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:121158400-121163600	Weak transcription	Small Intestine	intestine
3	chr12:121160200-121163600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:121162600-121163600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:121162800-121163600	Enhancers	Spleen	Spleen
6	chr12:121162800-121163800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:121163000-121163600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:121163000-121163600	Weak transcription	Gastric	stomach
9	chr12:121163000-121163600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr12:121163000-121163600	Flanking Active TSS	Dnd41	blood
11	chr12:121163000-121164000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:121163000-121164000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:121163000-121164000	Active TSS	Primary T cells from cord blood	blood
14	chr12:121163000-121164000	Active TSS	A549	lung
15	chr12:121163000-121164200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr12:121163000-121164200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr12:121163000-121164200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:121163000-121164400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr12:121163000-121164400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:121163000-121164600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:121163000-121164600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:121163000-121165000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr12:121163200-121163600	Flanking Active TSS	Liver	Liver
24	chr12:121163200-121163800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr12:121163200-121164000	Active TSS	H1 Cell Line	embryonic stem cell
26	chr12:121163200-121164000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:121163200-121164000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:121163200-121164000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:121163200-121164000	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr12:121163200-121164000	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr12:121163200-121164000	Active TSS	Aorta	Aorta
32	chr12:121163200-121164000	Active TSS	Brain Germinal Matrix	brain
33	chr12:121163200-121164000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:121163200-121164000	Active TSS	Right Ventricle	heart
35	chr12:121163200-121164000	Active TSS	HSMMtube	muscle
36	chr12:121163200-121164000	Active TSS	NHDF-Ad	bronchial
37	chr12:121163200-121164200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr12:121163200-121164200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:121163200-121164200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr12:121163200-121164200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:121163200-121164200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:121163200-121164200	Active TSS	Brain Angular Gyrus	brain
43	chr12:121163200-121164200	Active TSS	Brain Anterior Caudate	brain
44	chr12:121163200-121164200	Active TSS	Lung	lung
45	chr12:121163200-121164200	Flanking Active TSS	HMEC	breast
46	chr12:121163200-121164400	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr12:121163200-121164400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:121163200-121164400	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr12:121163200-121164400	Active TSS	Psoas Muscle	Psoas
50	chr12:121163200-121164400	Active TSS	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links