Variant report

Variant	rs3204635
Chromosome Location	chr12:57637593-57637594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:314)
CpG islands
(count:61)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:314 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:57637534-57637759	SK-N-SH_RA	brain:	n/a	n/a
2	TEAD4	chr12:57637373-57637847	K562	blood:	n/a	n/a
3	CTCF	chr12:57637560-57637710	GM12873	blood:	n/a	n/a
4	CTCF	chr12:57637560-57637710	GM12866	blood:	n/a	n/a
5	CTCF	chr12:57637465-57637819	Spleen_OC	spleen:	n/a	n/a
6	CTCF	chr12:57637540-57637690	SAEC	small airway:	n/a	n/a
7	ATF2	chr12:57637390-57637863	GM12878	blood:	n/a	chr12:57637650-57637664
8	CTCF	chr12:57637560-57637710	GM12865	blood:	n/a	n/a
9	CTCF	chr12:57637540-57637690	K562	blood:	n/a	n/a
10	CTCF	chr12:57637560-57637710	GM12872	blood:	n/a	n/a
11	UBTF	chr12:57637453-57637785	K562	blood:	n/a	n/a
12	TCF12	chr12:57636427-57637809	A549	lung:	n/a	chr12:57636563-57636573 chr12:57637747-57637757
13	CTCF	chr12:57637523-57637751	Kidney_OC	kidney:	n/a	n/a
14	CTCF	chr12:57637560-57637710	HCT-116	colon:	n/a	n/a
15	POLR2A	chr12:57637288-57637716	HCT-116	colon:	n/a	n/a
16	MAX	chr12:57637368-57638127	H1-hESC	embryonic stem cell:	n/a	n/a
17	NR2F2	chr12:57637415-57637949	K562	blood:	n/a	n/a
18	CTCF	chr12:57637520-57637670	GM12864	blood:	n/a	n/a
19	CTCF	chr12:57637520-57637670	HFF-Myc	foreskin:	n/a	n/a
20	MYC	chr12:57637556-57637701	MCF10A-Er-Src	breast:	n/a	n/a
21	CTCF	chr12:57637520-57637670	GM12873	blood:	n/a	n/a
22	RAD21	chr12:57637429-57637801	HepG2	liver:	n/a	n/a
23	CTCF	chr12:57637429-57637852	GM12878	blood:	n/a	n/a
24	CTCF	chr12:57637539-57637761	MCF-7	breast:	n/a	n/a
25	FOXM1	chr12:57637451-57637815	GM12878	blood:	n/a	n/a
26	CTCF	chr12:57637523-57637774	GM20000	blood:	n/a	n/a
27	SIN3A	chr12:57636523-57637762	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr12:57637540-57637690	WERI-Rb-1	eye:	n/a	n/a
29	POLR2A	chr12:57637454-57637629	Hela-S3	cervix:	n/a	n/a
30	ZBTB7A	chr12:57637227-57637763	K562	blood:	n/a	n/a
31	CTCF	chr12:57637560-57637710	HBMEC	blood vessel:	n/a	n/a
32	POLR2A	chr12:57637310-57637852	U87	brain:	n/a	n/a
33	CTCF	chr12:57637580-57637730	NB4	blood:	n/a	n/a
34	CTCF	chr12:57637540-57637690	A549	lung:	n/a	n/a
35	ZC3H11A	chr12:57637479-57637701	K562	blood:	n/a	n/a
36	CTCF	chr12:57637580-57637730	GM12869	blood:	n/a	n/a
37	RAD21	chr12:57637492-57637800	GM12878	blood:	n/a	n/a
38	BHLHE40	chr12:57637469-57637719	GM12878	blood:	n/a	n/a
39	RAD21	chr12:57637288-57637899	A549	lung:	n/a	n/a
40	MYC	chr12:57637530-57637953	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr12:57637520-57637768	Pancreas_OC	pancreas:	n/a	n/a
42	MAX	chr12:57637365-57637872	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr12:57637560-57637710	HCFaa	heart:	n/a	n/a
44	CTCF	chr12:57637540-57637690	Caco-2	colon:	n/a	n/a
45	YY1	chr12:57637255-57637852	H1-hESC	embryonic stem cell:	n/a	n/a
46	BHLHE40	chr12:57637495-57637728	K562	blood:	n/a	n/a
47	TFAP2C	chr12:57636725-57637653	Hela-S3	cervix:	n/a	chr12:57636963-57636978
48	ZNF263	chr12:57637436-57637829	HEK293-T-REx	kidney:	n/a	n/a
49	ATF2	chr12:57637375-57637844	H1-hESC	embryonic stem cell:	n/a	chr12:57637650-57637664
50	GTF2F1	chr12:57637472-57637762	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:57637574-57637624	HRPEpiC	eye:	n/a
2	chr12:57637574-57637624	HepG2	liver:	n/a
3	chr12:57637574-57637624	ovcar-3	ovarian:	n/a
4	chr12:57637574-57637624	BJ	skin:	n/a
5	chr12:57637574-57637624	MCF-7	breast:	n/a
6	chr12:57637574-57637624	NH-A	brain:	n/a
7	chr12:57637574-57637624	U87	brain:	n/a
8	chr12:57637574-57637624	CMK	blood:	n/a
9	chr12:57637574-57637624	HCPEpiC	choroid plexus:	n/a
10	chr12:57637574-57637624	AG04450	lung:	fetal
11	chr12:57637574-57637624	A549	lung:	n/a
12	chr12:57637574-57637624	NHBE	bronchial:	n/a
13	chr12:57637574-57637624	HPAEpiC	pulmonary alveolar:	n/a
14	chr12:57637574-57637624	H1-hESC	embryonic stem cell:	embryo
15	chr12:57637574-57637624	GM12891	blood:	n/a
16	chr12:57637574-57637624	T-47D	breast:	n/a
17	chr12:57637574-57637624	AG09309	skin:	n/a
18	chr12:57637574-57637624	NB4	blood:	n/a
19	chr12:57637574-57637624	GM12892	blood:	n/a
20	chr12:57637574-57637624	BE2_C	brain:	n/a
21	chr12:57637574-57637624	HCF	heart:	n/a
22	chr12:57637574-57637624	PrEC	prostate:	n/a
23	chr12:57637574-57637624	HAEpiC	amniotic membrane:	n/a
24	chr12:57637574-57637624	SAEC	small airway:	n/a
25	chr12:57637574-57637624	HUVEC	blood vessel:	n/a
26	chr12:57637574-57637624	HEK293	kidney:	embryo
27	chr12:57637574-57637624	GM12878	blood:	n/a
28	chr12:57637574-57637624	HRCEpiC	kidney:	n/a
29	chr12:57637574-57637624	SKMC	muscle:	n/a
30	chr12:57637574-57637624	GM19239	blood:	n/a
31	chr12:57637574-57637624	IMR90	lung:	fetal
32	chr12:57637574-57637624	NT2-D1	testis:	n/a
33	chr12:57637574-57637624	HEEpiC	esophagus:	n/a
34	chr12:57637574-57637624	HIPEpiC	eye:	n/a
35	chr12:57637574-57637624	Hela-S3	cervix:	n/a
36	chr12:57637574-57637624	AG10803	skin:	n/a
37	chr12:57637574-57637624	AG09319	gingival:	n/a
38	chr12:57637574-57637624	K562	blood:	n/a
39	chr12:57637574-57637624	RPTEC	kidney:	n/a
40	chr12:57637574-57637624	GM06990	blood:	n/a
41	chr12:57637574-57637624	ECC-1	luminal epithelium:	n/a
42	chr12:57637574-57637624	SK-N-MC	brain:	n/a
43	chr12:57637574-57637624	HMEC	breast:	n/a
44	chr12:57637574-57637624	PANC-1	pancreas:	n/a
45	chr12:57637574-57637624	PFSK-1	brain:	n/a
46	chr12:57637574-57637624	SK-N-SH	brain:	n/a
47	chr12:57637574-57637624	HNPCEpiC	eye:	n/a
48	chr12:57637574-57637624	NHDF-neo	bronchial:	n/a
49	chr12:57637574-57637624	HCM	heart:	n/a
50	chr12:57637574-57637624	SK-N-SH_RA	brain:	n/a

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57636021..57639018-chr12:57639327..57640991,2	MCF-7	breast:
2	chr12:57636648..57638491-chr12:57880305..57881901,2	K562	blood:
3	chr12:57608166..57609235-chr12:57637200..57637869,4	MCF-7	breast:
4	chr12:57637177..57638084-chr12:57849678..57850549,2	K562	blood:
5	chr12:57606643..57608087-chr12:57636460..57637985,5	MCF-7	breast:
6	chr12:57589437..57590373-chr12:57637167..57637902,2	K562	blood:
7	chr12:57635862..57639345-chr12:57850429..57852757,3	K562	blood:
8	chr12:57606466..57609055-chr12:57636459..57638396,24	K562	blood:
9	chr12:57637406..57639155-chr12:57645577..57649504,4	K562	blood:
10	chr12:57637439..57640284-chr12:57642882..57644600,2	MCF-7	breast:
11	chr12:57636983..57640050-chr12:57648004..57652445,5	K562	blood:
12	chr12:57633619..57639143-chr12:57853203..57857806,7	K562	blood:
13	chr12:57480680..57483745-chr12:57634924..57637654,3	MCF-7	breast:
14	chr12:57636584..57639625-chr12:57824200..57826164,3	K562	blood:
15	chr12:57636277..57638272-chr12:57641265..57643694,3	K562	blood:
16	chr12:57636584..57638482-chr12:57824121..57826164,3	K562	blood:
17	chr12:57478737..57483929-chr12:57633097..57638164,8	MCF-7	breast:
18	chr12:57632989..57634576-chr12:57636410..57638768,2	MCF-7	breast:
19	chr12:57606205..57609184-chr12:57636393..57638193,29	MCF-7	breast:
20	chr12:57636856..57639090-chr12:57822752..57824764,2	MCF-7	breast:
21	chr12:57637439..57639155-chr12:57645577..57647723,2	K562	blood:
22	chr12:57635469..57640213-chr12:57641305..57644273,5	K562	blood:
23	chr12:57609871..57610727-chr12:57636513..57637727,3	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFA4L2	TF binding region
NDUFA4L2	CpG island
ENSG00000111087	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000182379	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000185482	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000258001	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10876968	0.92[ASW][hapmap];0.95[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10876971	0.92[AFR][1000 genomes]
rs11172140	0.92[AFR][1000 genomes]
rs11172142	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11172155	1.00[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs11830804	0.83[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs12227309	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2943692	0.81[CEU][hapmap]
rs2943693	0.82[GIH][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap]
rs538548	0.83[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs567895	0.83[ASW][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs7133572	0.83[AFR][1000 genomes]
rs7302906	0.83[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7963352	0.92[AFR][1000 genomes]
rs7966846	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7976512	0.81[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3204635	CDKN2A	trans	lymphoblastoid	seeQTL
rs3204635	CDK4	cis	cerebellum	SCAN
rs3204635	SP7	cis	parietal	SCAN
rs3204635	SDR9C7	cis	cerebellum	SCAN
rs3204635	OR6C4	cis	parietal	SCAN
rs3204635	APOF	cis	parietal	SCAN
rs3204635	DNAJC14	cis	cerebellum	SCAN
rs3204635	OR6C1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57634600-57637800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:57634600-57638000	Bivalent Enhancer	Fetal Lung	lung
3	chr12:57635600-57637600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
4	chr12:57635600-57638600	Weak transcription	HSMMtube	muscle
5	chr12:57635800-57642600	Weak transcription	HSMM	muscle
6	chr12:57636200-57637600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr12:57636200-57637600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
8	chr12:57636200-57637600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
9	chr12:57636200-57637600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
10	chr12:57636200-57637800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr12:57636200-57638000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
12	chr12:57636200-57638000	Enhancers	Fetal Brain Male	brain
13	chr12:57636400-57637600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr12:57636400-57637600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:57636400-57637600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
16	chr12:57636400-57637600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
17	chr12:57636400-57637600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr12:57636400-57637600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
19	chr12:57636400-57637600	Bivalent/Poised TSS	HepG2	liver
20	chr12:57636400-57637600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
21	chr12:57636400-57637800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr12:57636400-57637800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr12:57636400-57637800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr12:57636400-57637800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr12:57636400-57637800	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:57636400-57637800	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr12:57636400-57637800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
28	chr12:57636400-57637800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:57636400-57637800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:57636400-57637800	Flanking Bivalent TSS/Enh	Thymus	Thymus
31	chr12:57636400-57637800	Enhancers	Spleen	Spleen
32	chr12:57636400-57638000	Flanking Active TSS	Dnd41	blood
33	chr12:57636600-57637600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
34	chr12:57636600-57637600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:57636600-57637600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
36	chr12:57636600-57637600	Flanking Bivalent TSS/Enh	Placenta	Placenta
37	chr12:57636600-57637600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr12:57636600-57637600	Enhancers	Lung	lung
39	chr12:57636600-57637600	Active TSS	Psoas Muscle	Psoas
40	chr12:57636600-57637600	Active TSS	Hela-S3	cervix
41	chr12:57636600-57637800	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr12:57636600-57637800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:57636600-57638000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr12:57636600-57638000	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr12:57636800-57637600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:57636800-57637600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:57636800-57637600	Enhancers	Fetal Heart	heart
48	chr12:57636800-57637800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:57636800-57637800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
50	chr12:57636800-57637800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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