Variant report

Variant	rs786448
Chromosome Location	chr12:124070214-124070215
allele	C/T
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	chr12:124070122-124070757	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:124068520-124070709	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:124069627-124073859	K562	blood:	n/a	n/a
4	POLR2A	chr12:124070174-124070469	HepG2	liver:	n/a	n/a
5	CEBPB	chr12:124070005-124070446	HepG2	liver:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
6	POLR2A	chr12:124069686-124070761	GM12878	blood:	n/a	n/a
7	CTCF	chr12:124070120-124070270	AG09319	gingival:	n/a	n/a
8	CEBPB	chr12:124070004-124070702	IMR90	lung:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
9	TAL1	chr12:124069980-124070223	K562	blood:	n/a	n/a
10	CEBPB	chr12:124070019-124070439	K562	blood:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
11	MXI1	chr12:124068488-124070795	IMR90	lung:	n/a	n/a
12	POLR2A	chr12:124069625-124070734	PFSK-1	brain:	n/a	n/a
13	HCFC1	chr12:124068422-124070407	Hela-S3	cervix:	n/a	n/a
14	SMC3	chr12:124070024-124070333	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:124069888-124070634	K562	blood:	n/a	n/a
16	POLR2A	chr12:124068404-124070969	HepG2	liver:	n/a	n/a
17	MXI1	chr12:124068656-124070224	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:124070117-124070785	HepG2	liver:	n/a	n/a
19	CEBPB	chr12:124069973-124070401	Hela-S3	cervix:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
20	POLR2A	chr12:124070208-124070492	K562	blood:	n/a	n/a
21	CEBPB	chr12:124070174-124070338	HepG2	liver:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
22	STAT3	chr12:124070067-124070267	MCF10A-Er-Src	breast:	n/a	n/a
23	PML	chr12:124069588-124070488	K562	blood:	n/a	n/a
24	CEBPB	chr12:124070009-124070436	A549	lung:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
25	POLR2A	chr12:124068344-124070778	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr12:124068640-124070455	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:124069683-124070910	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:124070178-124070556	MCF-7	breast:	n/a	n/a
29	TBL1XR1	chr12:124070185-124070624	K562	blood:	n/a	n/a
30	CHD1	chr12:124068312-124070779	IMR90	lung:	n/a	chr12:124069693-124069700
31	POLR2A	chr12:124068407-124070326	MCF10A-Er-Src	breast:	n/a	n/a
32	JUN	chr12:124068570-124070748	K562	blood:	n/a	chr12:124070434-124070446
33	MXI1	chr12:124067740-124070353	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr12:124068549-124070907	IMR90	lung:	n/a	n/a
35	CEBPB	chr12:124069886-124070492	A549	lung:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
36	MAZ	chr12:124068549-124070932	IMR90	lung:	n/a	n/a
37	HEY1	chr12:124070093-124070425	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123755285..123757528-chr12:124068793..124071301,3	MCF-7	breast:
2	chr12:123941098..123944051-chr12:124068238..124070527,2	K562	blood:
3	chr12:124067567..124070616-chr12:124116717..124118360,3	K562	blood:
4	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
5	chr12:124068831..124072178-chr12:124116882..124120107,5	K562	blood:
6	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
7	chr12:123941578..123944282-chr12:124067320..124071098,9	MCF-7	breast:
8	chr12:123846861..123850261-chr12:124066655..124071408,9	MCF-7	breast:
9	chr12:124016749..124018606-chr12:124069216..124071514,2	K562	blood:
10	chr12:123847713..123850022-chr12:124067528..124071055,3	MCF-7	breast:
11	chr12:123753500..123755086-chr12:124068992..124070507,2	MCF-7	breast:
12	chr12:124018224..124020563-chr12:124065688..124070487,5	K562	blood:
13	chr12:123872778..123876196-chr12:124065295..124071344,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247373	TF binding region
ENSG00000111361	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1051793	0.80[CEU][hapmap]
rs1060637	0.88[CEU][hapmap]
rs10846531	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs10846535	0.89[CEU][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10846537	0.85[CEU][hapmap]
rs11057307	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057320	0.80[EUR][1000 genomes]
rs11572920	0.88[CEU][hapmap]
rs11572952	0.81[CEU][hapmap]
rs11609591	0.89[CEU][hapmap]
rs11611354	0.85[CEU][hapmap]
rs11612030	0.88[CEU][hapmap]
rs11612479	0.85[CEU][hapmap]
rs11612927	0.84[CEU][hapmap]
rs11613632	0.84[CEU][hapmap]
rs11615300	0.81[EUR][1000 genomes]
rs12817757	0.84[CEU][hapmap]
rs12820195	0.85[CEU][hapmap]
rs12821242	0.87[CEU][hapmap]
rs12827074	0.85[CEU][hapmap]
rs12829893	0.88[CEU][hapmap]
rs12830927	0.88[CEU][hapmap]
rs1515814	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1515815	0.88[CEU][hapmap]
rs2048802	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2222060	0.81[CEU][hapmap]
rs2250026	0.85[CEU][hapmap]
rs3748268	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs3748269	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930708	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs6488883	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488888	0.81[CEU][hapmap]
rs6488893	0.85[CEU][hapmap]
rs6488897	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs6551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133199	0.88[CEU][hapmap]
rs7134074	0.88[CEU][hapmap]
rs7134896	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135660	0.84[CEU][hapmap]
rs7136939	0.85[CEU][hapmap]
rs7137946	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs7139193	0.92[CEU][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs7294984	0.81[CEU][hapmap]
rs7297576	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7298440	0.85[CEU][hapmap]
rs7298831	0.88[CEU][hapmap]
rs7302183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302649	0.85[CEU][hapmap]
rs7306549	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7307008	0.88[CEU][hapmap]
rs7307343	0.85[CEU][hapmap]
rs7308234	0.82[CEU][hapmap]
rs7308862	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7309528	0.85[CEU][hapmap]
rs7310918	0.85[CEU][hapmap]
rs7313032	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7313261	0.89[CEU][hapmap]
rs7313628	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7399224	0.85[CEU][hapmap]
rs786422	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786444	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7953599	0.85[CEU][hapmap]
rs7958693	0.92[CEU][hapmap];0.84[MEX][hapmap]
rs7959553	0.84[CEU][hapmap]
rs7963968	0.85[CEU][hapmap]
rs7964443	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7966867	0.92[CEU][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs7966882	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7972413	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7973155	0.84[CEU][hapmap]
rs7973695	0.84[CEU][hapmap]
rs7974279	0.89[CEU][hapmap]
rs7975119	0.85[CEU][hapmap]
rs7975233	0.85[CEU][hapmap]
rs7978447	0.85[CEU][hapmap]
rs7979528	0.85[CEU][hapmap]
rs884892	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs908373	0.92[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9919	0.83[GIH][hapmap]

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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' 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	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs786448	CABP1	cis	cerebellum	SCAN
rs786448	DDX55	cis	parietal	SCAN
rs786448	TCTN2	cis	Adipose Subcutaneous	GTEx
rs786448	ABCB9	cis	parietal	SCAN
rs786448	SETD1B	cis	parietal	SCAN
rs786448	TCTN2	cis	cerebellum	SCAN
rs786448	TCTN2	cis	Artery Tibial	GTEx
rs786448	TCTN2	cis	parietal	SCAN
rs786448	DDX55	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124067000-124070400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:124067200-124070400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:124067200-124070600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:124067400-124070800	Active TSS	NHLF	lung
5	chr12:124067600-124070400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:124067600-124070400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:124067600-124071400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:124068000-124070600	Active TSS	Right Ventricle	heart
9	chr12:124069400-124070400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr12:124069400-124070400	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr12:124069400-124070600	Active TSS	Right Atrium	heart
12	chr12:124069600-124070400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:124069600-124070400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr12:124069600-124070400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr12:124069600-124070400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr12:124069600-124070400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:124069600-124070400	Flanking Active TSS	Liver	Liver
18	chr12:124069600-124070400	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr12:124069600-124070400	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr12:124069600-124070400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr12:124069600-124070400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr12:124069600-124070400	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr12:124069600-124070600	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr12:124069600-124070600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr12:124069600-124070600	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr12:124069600-124070600	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr12:124069600-124070600	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr12:124069600-124070600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr12:124069600-124070800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:124069800-124070400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:124069800-124070400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:124069800-124070400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr12:124069800-124070400	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr12:124069800-124070400	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr12:124069800-124070400	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr12:124069800-124070400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:124069800-124070400	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr12:124069800-124070400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr12:124069800-124070400	Flanking Active TSS	Fetal Brain Female	brain
40	chr12:124069800-124070400	Flanking Active TSS	Fetal Heart	heart
41	chr12:124069800-124070400	Flanking Active TSS	Fetal Stomach	stomach
42	chr12:124069800-124070400	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr12:124069800-124070400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr12:124069800-124070400	Flanking Active TSS	Thymus	Thymus
45	chr12:124069800-124070400	Flanking Active TSS	GM12878-XiMat	blood
46	chr12:124069800-124070600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:124069800-124070600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:124069800-124070600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:124069800-124070600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:124069800-124070600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links