Variant report

Variant	rs7978656
Chromosome Location	chr12:120634289-120634290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:125)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr12:120631413-120634490	Hela-S3	cervix:	n/a	n/a
2	EP300	chr12:120633590-120634478	A549	lung:	n/a	n/a
3	BCLAF1	chr12:120632248-120634467	K562	blood:	n/a	chr12:120632625-120632638 chr12:120632581-120632594 chr12:120632462-120632475 chr12:120632464-120632477 chr12:120632577-120632590
4	BCLAF1	chr12:120633480-120634354	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:120631371-120639781	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr12:120632180-120634392	GM12878	blood:	n/a	n/a
7	NFATC1	chr12:120632249-120634334	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:120632048-120635920	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:120632029-120639863	Hela-S3	cervix:	n/a	n/a
10	PML	chr12:120633490-120634588	K562	blood:	n/a	n/a
11	TEAD4	chr12:120632311-120634578	K562	blood:	n/a	n/a
12	POLR2A	chr12:120632039-120634607	HL-60	blood:	n/a	n/a
13	POLR2A	chr12:120633434-120634425	HepG2	liver:	n/a	n/a
14	NR2F2	chr12:120632627-120634459	K562	blood:	n/a	n/a
15	USF2	chr12:120633534-120634365	Hela-S3	cervix:	n/a	n/a
16	HEY1	chr12:120632172-120634550	HepG2	liver:	n/a	chr12:120632300-120632315 chr12:120632461-120632476 chr12:120632302-120632317
17	NFIC	chr12:120632319-120634313	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:120632135-120635622	GM12891	blood:	n/a	n/a
19	JUND	chr12:120632335-120634322	A549	lung:	n/a	chr12:120632847-120632857 chr12:120632847-120632857 chr12:120632847-120632857 chr12:120632469-120632478
20	POLR2A	chr12:120632197-120634391	NB4	blood:	n/a	n/a
21	POLR2A	chr12:120631995-120634412	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:120632203-120639596	K562	blood:	n/a	n/a
23	POLR2A	chr12:120632246-120634551	HCT-116	colon:	n/a	n/a
24	POLR2A	chr12:120631403-120634540	ECC-1	luminal epithelium:	n/a	n/a
25	ELF1	chr12:120633447-120634500	A549	lung:	n/a	n/a
26	POLR2A	chr12:120632153-120635516	HepG2	liver:	n/a	n/a
27	TEAD4	chr12:120633740-120634299	HepG2	liver:	n/a	n/a
28	CEBPD	chr12:120633387-120634494	K562	blood:	n/a	n/a
29	MAX	chr12:120634061-120634343	K562	blood:	n/a	chr12:120634196-120634206
30	MAX	chr12:120632106-120634314	HCT-116	colon:	n/a	chr12:120632554-120632563 chr12:120634196-120634206
31	MAX	chr12:120633710-120634481	A549	lung:	n/a	chr12:120634196-120634206
32	POLR2A	chr12:120632269-120635730	HepG2	liver:	n/a	n/a
33	POLR2A	chr12:120632286-120635888	K562	blood:	n/a	n/a
34	MYC	chr12:120633977-120634422	MCF10A-Er-Src	breast:	n/a	chr12:120634196-120634206
35	POLR2A	chr12:120632158-120635679	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:120631475-120639779	H1-hESC	embryonic stem cell:	n/a	n/a
37	TCF12	chr12:120631656-120634398	A549	lung:	n/a	chr12:120631705-120631715
38	POLR2A	chr12:120632190-120639605	GM12892	blood:	n/a	n/a
39	CBX3	chr12:120633441-120634320	K562	blood:	n/a	n/a
40	MBD4	chr12:120633820-120634318	HepG2	liver:	n/a	n/a
41	CHD2	chr12:120632291-120634308	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr12:120632154-120635675	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:120631706-120635875	HepG2	liver:	n/a	n/a
44	POLR2A	chr12:120632217-120635677	GM12891	blood:	n/a	n/a
45	POLR2A	chr12:120632031-120639569	GM12892	blood:	n/a	n/a
46	POLR2A	chr12:120632229-120634398	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:120631711-120635880	MCF10A-Er-Src	breast:	n/a	n/a
48	CHD2	chr12:120632142-120634329	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr12:120632192-120634428	GM18505	blood:	n/a	n/a
50	POLR2A	chr12:120632260-120635714	GM12891	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120628864..120642103-chr12:120725347..120732286,54	K562	blood:
2	chr12:120628211..120641965-chr12:120660551..120674110,39	K562	blood:
3	chr12:120553299..120556376-chr12:120632430..120634315,3	MCF-7	breast:
4	chr12:120551826..120556882-chr12:120630846..120640383,26	K562	blood:
5	chr12:120634142..120641127-chr12:120698850..120705439,14	K562	blood:
6	chr12:120626707..120642605-chr12:120719450..120732919,96	MCF-7	breast:
7	chr12:120573945..120575639-chr12:120632409..120634633,3	MCF-7	breast:
8	chr12:120551430..120553069-chr12:120632996..120634781,2	MCF-7	breast:
9	chr12:120632665..120634375-chr12:120655462..120658221,2	K562	blood:
10	chr12:120600039..120601830-chr12:120632774..120634294,2	MCF-7	breast:
11	chr12:120574047..120576744-chr12:120631730..120634976,3	MCF-7	breast:
12	chr12:120632971..120634754-chr12:120762864..120765593,2	MCF-7	breast:
13	chr12:120632974..120634618-chr17:46971835..46974020,2	K562	blood:
14	chr12:120594749..120596361-chr12:120632172..120634549,2	K562	blood:
15	chr12:120562076..120563996-chr12:120632946..120634674,2	K562	blood:
16	chr12:120631139..120640506-chr12:120724902..120734482,54	K562	blood:
17	chr12:120552161..120556177-chr12:120630368..120635589,11	K562	blood:
18	chr12:120633014..120635461-chr17:64959552..64961225,2	MCF-7	breast:

No data

Variant related genes	Relation type
PXN-AS1	TF binding region
GCN1L1	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000170890	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000075461	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000159199	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000089154	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10735071	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774543	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12308065	0.92[ASN][1000 genomes]
rs2286046	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2696029	1.00[JPT][hapmap]
rs3845191	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847968	1.00[YRI][hapmap]
rs3956837	1.00[ASN][1000 genomes]
rs4503602	0.81[CEU][hapmap]
rs4766959	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4767884	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490287	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7298516	1.00[JPT][hapmap]
rs7960843	0.92[ASN][1000 genomes]
rs7968689	0.92[ASN][1000 genomes]
rs965791	1.00[JPT][hapmap]

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	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised 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	484 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7978656	GCN1L1	cis	cerebellum	SCAN
rs7978656	GCN1L1	cis	parietal	SCAN
rs7978656	CABP1	cis	cerebellum	SCAN
rs7978656	GCN1L1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120633000-120634400	Transcr. at gene 5' and 3'	A549	lung
2	chr12:120633000-120635400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:120633000-120637200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:120633000-120637800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:120633200-120634600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:120633200-120634600	Weak transcription	Aorta	Aorta
7	chr12:120633200-120635000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:120633200-120635400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:120633200-120635400	Weak transcription	Fetal Heart	heart
10	chr12:120633200-120635800	Weak transcription	Right Atrium	heart
11	chr12:120633200-120636200	Genic enhancers	NHLF	lung
12	chr12:120633200-120638400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:120633400-120634400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:120633400-120634600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:120633400-120634600	Weak transcription	Psoas Muscle	Psoas
16	chr12:120633400-120634800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:120633400-120634800	Weak transcription	Brain Angular Gyrus	brain
18	chr12:120633400-120634800	Strong transcription	Fetal Brain Female	brain
19	chr12:120633400-120635000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:120633400-120635800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:120633400-120636200	Genic enhancers	Adipose Nuclei	Adipose
22	chr12:120633400-120636200	Strong transcription	Fetal Lung	lung
23	chr12:120633400-120636400	Weak transcription	Fetal Brain Male	brain
24	chr12:120633400-120636800	Strong transcription	Fetal Stomach	stomach
25	chr12:120633400-120637200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr12:120633400-120637600	Genic enhancers	Liver	Liver
27	chr12:120633600-120634600	Genic enhancers	HUVEC	blood vessel
28	chr12:120633600-120634800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:120633600-120634800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:120633600-120634800	Genic enhancers	Muscle Satellite Cultured Cells	--
31	chr12:120633600-120634800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:120633600-120634800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:120633600-120634800	Genic enhancers	Osteobl	bone
34	chr12:120633600-120635000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:120633600-120635200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:120633600-120635200	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:120633600-120635400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:120633600-120635800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:120633600-120636000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:120633600-120636200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:120633600-120636200	Genic enhancers	HMEC	breast
42	chr12:120633600-120636400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:120633600-120636400	Strong transcription	Lung	lung
44	chr12:120633600-120637000	Genic enhancers	Fetal Thymus	thymus
45	chr12:120633600-120638000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
46	chr12:120633600-120638200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:120633800-120634400	Flanking Active TSS	Hela-S3	cervix
48	chr12:120633800-120634600	Weak transcription	Esophagus	oesophagus
49	chr12:120633800-120634800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:120633800-120634800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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