Variant report

Variant	rs11834109
Chromosome Location	chr12:48746220-48746221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr12:48746086-48746493	K562	blood:	n/a	n/a
2	UBTF	chr12:48746185-48746383	K562	blood:	n/a	n/a
3	E2F6	chr12:48746212-48746491	K562	blood:	n/a	n/a
4	MAX	chr12:48746215-48746602	K562	blood:	n/a	n/a
5	ARID3A	chr12:48746094-48746552	K562	blood:	n/a	n/a
6	JUND	chr12:48746115-48746577	K562	blood:	n/a	n/a
7	ELF1	chr12:48746189-48746572	K562	blood:	n/a	n/a
8	TBL1XR1	chr12:48746139-48746548	K562	blood:	n/a	n/a
9	USF1	chr12:48746139-48746595	K562	blood:	n/a	n/a
10	NR2F2	chr12:48745970-48746578	K562	blood:	n/a	n/a
11	POLR2A	chr12:48746133-48746656	K562	blood:	n/a	n/a
12	MXI1	chr12:48746199-48746412	K562	blood:	n/a	n/a
13	TAL1	chr12:48746014-48746530	K562	blood:	n/a	n/a
14	MYC	chr12:48746007-48746632	K562	blood:	n/a	n/a
15	TBP	chr12:48745892-48746513	K562	blood:	n/a	n/a
16	EP300	chr12:48746001-48746542	K562	blood:	n/a	n/a
17	MAX	chr12:48745651-48746540	K562	blood:	n/a	chr12:48745748-48745758 chr12:48745749-48745760
18	ATF1	chr12:48746092-48746501	K562	blood:	n/a	n/a
19	POLR2A	chr12:48746094-48746498	K562	blood:	n/a	n/a
20	POLR2A	chr12:48746038-48746439	K562	blood:	n/a	n/a
21	MAX	chr12:48746102-48746542	K562	blood:	n/a	n/a
22	MAFK	chr12:48746205-48746313	K562	blood:	n/a	n/a
23	UBTF	chr12:48746044-48746456	K562	blood:	n/a	n/a
24	GATA1	chr12:48746007-48746628	PBDE	blood:	n/a	n/a
25	ZC3H11A	chr12:48745938-48746565	K562	blood:	n/a	n/a
26	POLR2A	chr12:48746136-48746544	K562	blood:	n/a	n/a
27	BHLHE40	chr12:48746190-48746548	K562	blood:	n/a	n/a
28	HCFC1	chr12:48746200-48746513	K562	blood:	n/a	n/a
29	CEBPB	chr12:48746151-48746316	K562	blood:	n/a	n/a
30	CEBPD	chr12:48746129-48746559	K562	blood:	n/a	n/a
31	RCOR1	chr12:48746063-48746541	K562	blood:	n/a	n/a
32	POLR2A	chr12:48746086-48746521	K562	blood:	n/a	n/a
33	TEAD4	chr12:48746049-48746483	K562	blood:	n/a	n/a
34	CBX3	chr12:48745982-48746584	K562	blood:	n/a	n/a
35	YY1	chr12:48746106-48746436	K562	blood:	n/a	n/a
36	MAZ	chr12:48745705-48746493	K562	blood:	n/a	chr12:48745749-48745760
37	TBL1XR1	chr12:48746185-48746548	K562	blood:	n/a	n/a
38	POLR2A	chr12:48745848-48746237	MCF10A-Er-Src	breast:	n/a	n/a
39	USF1	chr12:48746112-48746655	K562	blood:	n/a	n/a
40	TEAD4	chr12:48745975-48746670	K562	blood:	n/a	n/a
41	MYC	chr12:48745733-48746637	K562	blood:	n/a	chr12:48745748-48745758 chr12:48745749-48745760
42	ZMIZ1	chr12:48746178-48746414	K562	blood:	n/a	n/a
43	STAT5A	chr12:48746044-48746550	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48592134..48593924-chr12:48746168..48749051,2	MCF-7	breast:
2	chr12:48740296..48746434-chr12:48748194..48754526,9	MCF-7	breast:
3	chr12:48744030..48746480-chr12:48749780..48752086,4	K562	blood:
4	chr12:48741301..48746348-chr12:48747901..48753728,9	MCF-7	breast:
5	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-H1FNT-1	chr12:48745031-48746610	NONHSAT027996

No data

Variant related genes	Relation type
ZNF641	TF binding region
ENSG00000257763	Chromatin interaction
ENSG00000269514	Chromatin interaction
ENSG00000258273	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1004746	1.00[CEU][hapmap]
rs10506276	0.85[CEU][hapmap]
rs10506277	1.00[CEU][hapmap]
rs10506278	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10506279	0.95[EUR][1000 genomes]
rs10506280	0.98[EUR][1000 genomes]
rs11830378	0.85[CEU][hapmap]
rs17122906	0.98[EUR][1000 genomes]
rs17122918	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17122920	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17224674	1.00[CEU][hapmap]
rs17224828	0.85[CEU][hapmap]
rs17225198	0.85[CEU][hapmap]
rs17225261	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17225366	0.80[EUR][1000 genomes]
rs17225751	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17226359	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17226506	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17226723	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17823193	0.85[CEU][hapmap]
rs17823415	0.85[CEU][hapmap]
rs17823565	0.85[CEU][hapmap]
rs17824200	0.84[EUR][1000 genomes]
rs17824705	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17824989	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17825013	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs55684363	0.89[EUR][1000 genomes]
rs55763362	0.93[EUR][1000 genomes]
rs55794326	0.84[EUR][1000 genomes]
rs55854069	0.89[EUR][1000 genomes]
rs55920439	0.98[EUR][1000 genomes]
rs56048326	0.82[EUR][1000 genomes]
rs56084718	1.00[EUR][1000 genomes]
rs56110736	0.98[EUR][1000 genomes]
rs56271815	1.00[EUR][1000 genomes]
rs56378318	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56383074	1.00[EUR][1000 genomes]
rs56389692	0.93[EUR][1000 genomes]
rs56412095	1.00[EUR][1000 genomes]
rs59724592	0.93[EUR][1000 genomes]
rs6580666	0.94[EUR][1000 genomes]
rs7297558	0.85[CEU][hapmap]
rs7301153	0.87[CEU][hapmap]
rs7301509	0.87[CEU][hapmap]
rs7307874	0.87[CEU][hapmap]
rs7310935	0.87[CEU][hapmap]
rs751315	1.00[EUR][1000 genomes]
rs751316	1.00[EUR][1000 genomes]
rs7966782	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv1045159	chr12:48730024-48748940	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48745200-48748400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:48745400-48747400	Weak transcription	HSMMtube	muscle
3	chr12:48745400-48755800	Weak transcription	Ovary	ovary
4	chr12:48745400-48757200	Weak transcription	Right Ventricle	heart
5	chr12:48745600-48746400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:48745600-48746400	Enhancers	Brain Angular Gyrus	brain
7	chr12:48745600-48746400	Enhancers	Colon Smooth Muscle	Colon
8	chr12:48745600-48746400	Enhancers	Left Ventricle	heart
9	chr12:48745600-48746400	Enhancers	Right Atrium	heart
10	chr12:48745600-48746600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr12:48745600-48746600	Enhancers	Lung	lung
12	chr12:48745600-48746600	Enhancers	Psoas Muscle	Psoas
13	chr12:48745600-48746600	Flanking Active TSS	K562	blood
14	chr12:48745600-48748400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:48745600-48750000	Weak transcription	NHEK	skin
16	chr12:48745600-48762400	Weak transcription	Aorta	Aorta
17	chr12:48745800-48746400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:48745800-48746400	Enhancers	Brain Substantia Nigra	brain
19	chr12:48745800-48746400	Enhancers	Small Intestine	intestine
20	chr12:48745800-48746400	Enhancers	Spleen	Spleen
21	chr12:48745800-48746600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:48745800-48746600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr12:48745800-48748200	Weak transcription	HMEC	breast
24	chr12:48745800-48750000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:48745800-48752200	Weak transcription	Fetal Intestine Small	intestine
26	chr12:48746000-48746400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:48746000-48746400	Enhancers	Brain Hippocampus Middle	brain
28	chr12:48746000-48746400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:48746000-48746400	Enhancers	Hela-S3	cervix
30	chr12:48746000-48746600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:48746000-48746600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr12:48746000-48746600	Enhancers	Rectal Smooth Muscle	rectum
33	chr12:48746000-48746800	Enhancers	Pancreas	Pancrea
34	chr12:48746000-48749800	Weak transcription	A549	lung
35	chr12:48746000-48750200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:48746000-48750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:48746000-48752800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:48746000-48756600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:48746200-48746600	Enhancers	Gastric	stomach
40	chr12:48746200-48746600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:48746200-48749800	Weak transcription	HepG2	liver
42	chr12:48746200-48754600	Weak transcription	Adipose Nuclei	Adipose
43	chr12:48746200-48756800	Weak transcription	Brain Anterior Caudate	brain
44	chr12:48746200-48757200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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