Variant report

Variant	rs11608804
Chromosome Location	chr12:48176102-48176103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48174429-48176133	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:48174640-48177283	K562	blood:	n/a	n/a
3	GATA3	chr12:48175593-48176112	T-47D	breast:	n/a	n/a
4	POLR2A	chr12:48174577-48176123	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:48174528-48176247	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:48174463-48176966	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:48174495-48178624	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr12:48175664-48176180	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr12:48168539-48189348	K562	blood:	n/a	n/a
10	POLR2A	chr12:48174698-48176170	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:48174566-48182409	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:48176051-48176548	A549	lung:	n/a	n/a
13	POLR2A	chr12:48174464-48176732	HUVEC	blood vessel:	n/a	n/a
14	FOS	chr12:48176086-48176238	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr12:48174560-48176569	U87	brain:	n/a	n/a
16	POLR2A	chr12:48174647-48178121	K562	blood:	n/a	n/a
17	POLR2A	chr12:48174558-48176397	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr12:48174622-48176936	HUVEC	blood vessel:	n/a	n/a
19	CCNT2	chr12:48175984-48176489	K562	blood:	n/a	n/a
20	EP300	chr12:48175483-48176110	T-47D	breast:	n/a	n/a
21	POLR2A	chr12:48174499-48178629	K562	blood:	n/a	n/a
22	POLR2A	chr12:48174596-48179981	K562	blood:	n/a	n/a
23	POLR2A	chr12:48175884-48176110	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:48174592-48181015	K562	blood:	n/a	n/a
25	JUND	chr12:48176083-48176460	A549	lung:	n/a	n/a
26	POLR2A	chr12:48174588-48177966	K562	blood:	n/a	n/a
27	POLR2A	chr12:48174624-48178557	K562	blood:	n/a	n/a
28	POLR2A	chr12:48172733-48176227	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr12:48175908-48176121	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:48174676-48178288	A549	lung:	n/a	n/a
31	POLR2A	chr12:48174497-48176547	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr12:48174490-48178696	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr12:48174562-48178245	Hela-S3	cervix:	n/a	n/a
34	BCL3	chr12:48175534-48176136	K562	blood:	n/a	n/a
35	POLR2A	chr12:48175616-48176164	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr12:48174465-48181100	K562	blood:	n/a	n/a
37	CTCF	chr12:48176000-48176150	SAEC	small airway:	n/a	n/a
38	CHD2	chr12:48175734-48176473	K562	blood:	n/a	n/a
39	POLR2A	chr12:48174620-48176420	K562	blood:	n/a	n/a
40	POLR2A	chr12:48174512-48177433	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr12:48174631-48176465	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:48174642-48178463	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48173549..48176410-chr12:48184370..48186817,3	K562	blood:
2	chr12:48175695..48177408-chr12:48190225..48192647,2	K562	blood:
3	chr12:48164603..48170216-chr12:48170812..48178110,12	MCF-7	breast:
4	chr12:48175648..48178866-chr12:48181283..48184772,5	MCF-7	breast:
5	chr12:48174794..48177034-chr12:48211084..48213999,3	MCF-7	breast:
6	chr12:48135925..48137862-chr12:48173853..48176277,2	MCF-7	breast:
7	chr12:48173236..48178017-chr12:48212091..48216621,8	MCF-7	breast:
8	chr12:48111607..48113554-chr12:48173778..48176264,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268069	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000111405	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2240108	0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3759408	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7138076	0.86[ASN][1000 genomes]
rs73105899	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73107911	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7485961	0.86[EUR][1000 genomes];0.83[ASN][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	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS 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
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48168000-48177200	Weak transcription	Small Intestine	intestine
2	chr12:48168200-48195200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:48168600-48178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:48169000-48177600	Weak transcription	Dnd41	blood
5	chr12:48169200-48177600	Weak transcription	Fetal Lung	lung
6	chr12:48169200-48178600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:48169400-48179200	Weak transcription	Fetal Kidney	kidney
8	chr12:48169800-48181200	Weak transcription	GM12878-XiMat	blood
9	chr12:48170600-48181200	Weak transcription	HepG2	liver
10	chr12:48172200-48177600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:48172400-48176200	Weak transcription	HUVEC	blood vessel
12	chr12:48172400-48177400	Weak transcription	HSMMtube	muscle
13	chr12:48173000-48177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:48173000-48177000	Weak transcription	Psoas Muscle	Psoas
15	chr12:48173000-48192400	Weak transcription	Right Atrium	heart
16	chr12:48173200-48176200	Weak transcription	Fetal Brain Male	brain
17	chr12:48173200-48176600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:48173200-48177600	Genic enhancers	Brain Substantia Nigra	brain
19	chr12:48173200-48177800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr12:48173200-48180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:48173200-48191200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:48173400-48178000	Genic enhancers	Brain Inferior Temporal Lobe	brain
23	chr12:48173400-48180400	Strong transcription	Fetal Intestine Small	intestine
24	chr12:48173600-48176200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:48173600-48176400	Strong transcription	A549	lung
26	chr12:48173600-48176800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:48173600-48177000	Genic enhancers	Brain Anterior Caudate	brain
28	chr12:48173600-48177200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:48173600-48178600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:48173600-48180400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:48173600-48187600	Weak transcription	Fetal Heart	heart
32	chr12:48173800-48176800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:48173800-48176800	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:48173800-48176800	Strong transcription	Fetal Muscle Leg	muscle
35	chr12:48173800-48178000	Genic enhancers	Brain Hippocampus Middle	brain
36	chr12:48173800-48178200	Genic enhancers	Brain Cingulate Gyrus	brain
37	chr12:48173800-48178400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr12:48173800-48193800	Strong transcription	Gastric	stomach
39	chr12:48173800-48195400	Strong transcription	Fetal Stomach	stomach
40	chr12:48174000-48177000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:48174000-48193000	Strong transcription	Placenta	Placenta
42	chr12:48174200-48176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:48174200-48177400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:48174600-48191600	Strong transcription	Thymus	Thymus
45	chr12:48174600-48192200	Strong transcription	Lung	lung
46	chr12:48174600-48192600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:48174600-48193200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:48174600-48193400	Strong transcription	Brain Germinal Matrix	brain
49	chr12:48174600-48195600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:48174800-48178200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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