Variant report

Variant	rs11054842
Chromosome Location	chr12:12509865-12509866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:433)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:433 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr12:12509700-12510292	GM12878	blood:	n/a	chr12:12510100-12510114
2	CHD2	chr12:12509793-12510122	H1-hESC	embryonic stem cell:	n/a	n/a
3	RCOR1	chr12:12509563-12510280	K562	blood:	n/a	n/a
4	ZNF143	chr12:12509742-12510206	H1-hESC	embryonic stem cell:	n/a	n/a
5	HEY1	chr12:12509700-12510555	K562	blood:	n/a	chr12:12510210-12510225 chr12:12510312-12510327
6	POLR2A	chr12:12509622-12511096	NB4	blood:	n/a	n/a
7	REST	chr12:12509471-12510731	A549	lung:	n/a	chr12:12510491-12510504
8	MYC	chr12:12509700-12510386	MCF10A-Er-Src	breast:	n/a	chr12:12510147-12510156
9	POLR2A	chr12:12509692-12510868	GM19193	blood:	n/a	n/a
10	POLR2A	chr12:12509737-12510623	Gliobla	brain:	n/a	n/a
11	POLR2A	chr12:12509361-12511865	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:12509528-12511290	PBDE	blood:	n/a	n/a
13	E2F6	chr12:12509463-12510730	A549	lung:	n/a	chr12:12510323-12510332 chr12:12510163-12510172 chr12:12510205-12510217 chr12:12510324-12510334
14	ELF1	chr12:12509728-12510212	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:12509693-12510778	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:12509754-12510317	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3AK20	chr12:12509586-12510565	HCT-116	colon:	n/a	n/a
18	MAX	chr12:12509759-12510720	H1-hESC	embryonic stem cell:	n/a	chr12:12510147-12510156
19	EP300	chr12:12509692-12510552	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:12509711-12510648	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr12:12509740-12510224	SK-N-SH_RA	brain:	n/a	n/a
22	GABPA	chr12:12509602-12510309	A549	lung:	n/a	n/a
23	TBP	chr12:12509661-12510346	GM12878	blood:	n/a	n/a
24	ELF1	chr12:12509759-12510252	K562	blood:	n/a	n/a
25	TAF1	chr12:12509707-12510302	PFSK-1	brain:	n/a	n/a
26	MXI1	chr12:12509291-12510977	IMR90	lung:	n/a	n/a
27	POLR2A	chr12:12509689-12510732	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:12509648-12510356	PANC-1	pancreas:	n/a	n/a
29	ELK1	chr12:12509745-12510215	K562	blood:	n/a	n/a
30	REST	chr12:12509668-12510252	A549	lung:	n/a	n/a
31	POLR2A	chr12:12509782-12510553	A549	lung:	n/a	n/a
32	POU2F2	chr12:12509717-12510349	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:12509442-12511869	GM18505	blood:	n/a	n/a
34	HMGN3	chr12:12509799-12510382	K562	blood:	n/a	n/a
35	TAF7	chr12:12509723-12510351	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:12509736-12510741	GM12891	blood:	n/a	n/a
37	MYC	chr12:12509669-12510714	K562	blood:	n/a	chr12:12510147-12510156
38	TBL1XR1	chr12:12509513-12511293	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:12509637-12510832	HL-60	blood:	n/a	n/a
40	TBP	chr12:12509716-12510270	HepG2	liver:	n/a	n/a
41	ETS1	chr12:12509632-12510296	A549	lung:	n/a	n/a
42	ELF1	chr12:12509598-12510433	SK-N-SH	brain:	n/a	chr12:12510322-12510334
43	RUNX3	chr12:12509506-12510741	GM12878	blood:	n/a	n/a
44	IRF1	chr12:12509675-12510262	K562	blood:	n/a	n/a
45	E2F4	chr12:12509804-12510305	GM12878	blood:	n/a	chr12:12510163-12510172 chr12:12510205-12510217
46	GABPA	chr12:12509827-12510274	HepG2	liver:	n/a	n/a
47	JUND	chr12:12509728-12510163	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF12	chr12:12509695-12510305	A549	lung:	n/a	chr12:12510084-12510091
49	POLR2A	chr12:12509864-12510452	HepG2	liver:	n/a	n/a
50	YY1	chr12:12509837-12510132	A549	lung:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:12507773..12511633-chr12:12848137..12852132,5	K562	blood:
2	chr12:12507988..12510235-chr12:12714031..12716523,2	MCF-7	breast:
3	chr12:12509822..12510620-chr20:34252555..34253334,2	NB4	blood:
4	chr12:12502870..12504833-chr12:12508269..12511200,3	K562	blood:
5	chr12:12509599..12512153-chr12:12848294..12850312,2	MCF-7	breast:
6	chr12:12419774..12421330-chr12:12508637..12511348,2	MCF-7	breast:
7	chr12:12509167..12512867-chr12:12713185..12715471,5	MCF-7	breast:
8	chr12:12501083..12504981-chr12:12508403..12511914,10	MCF-7	breast:
9	chr12:12507394..12509953-chr12:12633944..12635631,2	MCF-7	breast:
10	chr12:12501756..12503820-chr12:12509545..12511706,2	MCF-7	breast:
11	chr12:12508678..12514314-chr12:12868637..12874427,7	K562	blood:
12	chr12:12509330..12511597-chr12:12874960..12877485,2	K562	blood:
13	chr12:12508799..12512106-chr12:12876417..12880418,4	MCF-7	breast:
14	chr12:12509229..12511438-chr12:12866532..12868285,2	MCF-7	breast:
15	chr12:12509330..12513233-chr12:12874960..12880946,8	K562	blood:
16	chr12:12508122..12513324-chr12:12871018..12878415,8	MCF-7	breast:
17	chr12:12502870..12505613-chr12:12507814..12511200,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC007621.1-1	chr12:12509862-12510001	XLOC_010020
2	lnc-AC007621.1-1	chr12:12509862-12510001	NR_024061

No data

Variant related genes	Relation type
LOH12CR1	TF binding region
ENSG00000111276	Chromatin interaction
ENSG00000183150	Chromatin interaction
ENSG00000256658	Chromatin interaction
ENSG00000111261	Chromatin interaction
ENSG00000178878	Chromatin interaction
ENSG00000244462	Chromatin interaction
ENSG00000070018	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000214078	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11054828	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11054831	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11054843	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11054847	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1544683	0.90[ASN][1000 genomes]
rs16907939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34584825	0.90[ASN][1000 genomes]
rs34635703	0.90[ASN][1000 genomes]
rs36058772	0.88[ASN][1000 genomes]
rs71457145	0.90[ASN][1000 genomes]
rs7969816	0.86[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1036040	chr12:12506839-12541869	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1037542	chr12:12506839-12542868	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1045637	chr12:12506839-12546747	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12503800-12510000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:12504400-12510000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:12504800-12510000	Weak transcription	Small Intestine	intestine
4	chr12:12507200-12510000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:12509200-12510600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:12509200-12511200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:12509400-12510000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr12:12509400-12510000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr12:12509400-12510000	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr12:12509400-12510000	Flanking Active TSS	Dnd41	blood
11	chr12:12509400-12510000	Flanking Active TSS	Osteobl	bone
12	chr12:12509400-12510200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:12509400-12510200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:12509400-12510400	Active TSS	Placenta Amnion	Placenta Amnion
15	chr12:12509400-12510600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:12509400-12510600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:12509400-12510800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:12509400-12510800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:12509400-12510800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr12:12509400-12510800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:12509400-12510800	Active TSS	Rectal Smooth Muscle	rectum
22	chr12:12509400-12510800	Active TSS	HSMMtube	muscle
23	chr12:12509400-12511200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr12:12509400-12511400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr12:12509400-12511400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:12509400-12511400	Active TSS	Pancreas	Pancrea
27	chr12:12509400-12511400	Active TSS	Psoas Muscle	Psoas
28	chr12:12509400-12511600	Flanking Active TSS	HMEC	breast
29	chr12:12509400-12511800	Active TSS	Right Atrium	heart
30	chr12:12509600-12510000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:12509600-12510000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:12509600-12510000	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr12:12509600-12510000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr12:12509600-12510000	Flanking Active TSS	Liver	Liver
35	chr12:12509600-12510000	Flanking Active TSS	Fetal Brain Male	brain
36	chr12:12509600-12510000	Flanking Active TSS	Fetal Thymus	thymus
37	chr12:12509600-12510000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:12509600-12510000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr12:12509600-12510000	Flanking Active TSS	NHEK	skin
40	chr12:12509600-12510600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
41	chr12:12509600-12510600	Active TSS	Fetal Muscle Leg	muscle
42	chr12:12509600-12510600	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr12:12509600-12510600	Active TSS	HUVEC	blood vessel
44	chr12:12509600-12510800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:12509600-12510800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:12509600-12510800	Active TSS	Colon Smooth Muscle	Colon
47	chr12:12509600-12510800	Active TSS	Duodenum Mucosa	Duodenum
48	chr12:12509600-12510800	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr12:12509600-12510800	Active TSS	Fetal Intestine Large	intestine
50	chr12:12509600-12510800	Active TSS	Fetal Kidney	kidney

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