Variant report

Variant	rs1108124
Chromosome Location	chr12:39299614-39299615
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	chr12:39298240-39300998	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:39298530-39300103	GM18526	blood:	n/a	n/a
3	SP1	chr12:39299113-39299675	GM12878	blood:	n/a	chr12:39299581-39299595 chr12:39299467-39299481 chr12:39299471-39299485 chr12:39299443-39299457
4	CTCF	chr12:39299500-39299650	HRPEpiC	eye:	n/a	chr12:39299584-39299597
5	CTBP2	chr12:39298666-39300802	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr12:39298724-39299881	K562	blood:	n/a	chr12:39299472-39299483
7	POLR2A	chr12:39298499-39299777	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr12:39298999-39299661	H1-hESC	embryonic stem cell:	n/a	n/a
9	SMARCC2	chr12:39298655-39300915	Hela-S3	cervix:	n/a	chr12:39298980-39298989
10	CTCF	chr12:39299500-39299650	AG09319	gingival:	n/a	chr12:39299584-39299597
11	POLR2A	chr12:39298438-39300048	PANC-1	pancreas:	n/a	n/a
12	USF2	chr12:39298806-39299677	H1-hESC	embryonic stem cell:	n/a	chr12:39299075-39299086
13	KAP1	chr12:39298557-39299778	U2OS	brain:	n/a	n/a
14	TBP	chr12:39299329-39299935	GM12878	blood:	n/a	n/a
15	MAX	chr12:39298581-39300012	HepG2	liver:	n/a	n/a
16	STAT1	chr12:39298642-39300035	GM12878	blood:	n/a	chr12:39299472-39299484 chr12:39299012-39299020 chr12:39299477-39299489 chr12:39299214-39299226 chr12:39299012-39299035 chr12:39299219-39299231 chr12:39298834-39298841
17	MAX	chr12:39298545-39300836	GM12878	blood:	n/a	chr12:39300641-39300651 chr12:39300127-39300137
18	PAX5	chr12:39299310-39299832	GM12892	blood:	n/a	n/a
19	POLR2A	chr12:39298411-39301114	GM19193	blood:	n/a	n/a
20	SMARCC1	chr12:39298667-39301343	Hela-S3	cervix:	n/a	chr12:39298980-39298989
21	RUNX3	chr12:39298529-39300182	GM12878	blood:	n/a	n/a
22	HA-E2F1	chr12:39298894-39299805	Hela-S3	cervix:	n/a	n/a
23	ZNF143	chr12:39299073-39299945	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:39298617-39300930	GM12891	blood:	n/a	n/a
25	REST	chr12:39298659-39299761	U87	brain:	n/a	chr12:39299602-39299612
26	POLR2A	chr12:39298523-39299906	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr12:39299067-39299769	A549	lung:	n/a	n/a
28	ATF3	chr12:39299347-39299915	A549	lung:	n/a	n/a
29	FOS	chr12:39299527-39299656	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr12:39298494-39300111	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:39298502-39300996	GM18951	blood:	n/a	n/a
32	PML	chr12:39299193-39299763	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:39298609-39300763	HEK293	kidney:	n/a	n/a
34	POLR2A	chr12:39298459-39300162	GM12891	blood:	n/a	n/a
35	KAP1	chr12:39298516-39301267	HEK293	kidney:	n/a	n/a
36	POLR2A	chr12:39298623-39300890	GM12878	blood:	n/a	n/a
37	SMC3	chr12:39299207-39299946	GM12878	blood:	n/a	n/a
38	UBTF	chr12:39298725-39299761	K562	blood:	n/a	n/a
39	POLR2A	chr12:39298408-39300010	PFSK-1	brain:	n/a	n/a
40	CTCF	chr12:39299600-39299750	HCT-116	colon:	n/a	n/a
41	RCOR1	chr12:39298615-39300036	GM12878	blood:	n/a	n/a
42	RFX5	chr12:39298646-39299661	GM12878	blood:	n/a	chr12:39298797-39298812 chr12:39298800-39298809 chr12:39298798-39298812
43	CTCF	chr12:39299503-39301028	SK-N-SH	brain:	n/a	chr12:39299584-39299597 chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
44	CREB1	chr12:39298547-39299672	A549	lung:	n/a	n/a
45	MAZ	chr12:39298595-39300026	K562	blood:	n/a	n/a
46	POLR2A	chr12:39298620-39299820	PBDE	blood:	n/a	n/a
47	CTCF	chr12:39299580-39299730	Hela-S3	cervix:	n/a	chr12:39299584-39299597
48	POLR2A	chr12:39298537-39299874	HCT-116	colon:	n/a	n/a
49	JUND	chr12:39298593-39299841	A549	lung:	n/a	chr12:39298719-39298733 chr12:39298978-39298990 chr12:39299064-39299073 chr12:39298980-39298988
50	POLR2A	chr12:39298444-39301299	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:39299154..39299960-chr4:40632090..40632777,2	Hela-S3	cervix:
2	chr12:39299427..39300247-chr6:17706649..17707521,2	Hela-S3	cervix:
3	chr12:39299074..39299955-chr9:26892301..26892993,2	Hela-S3	cervix:

Variant related genes	Relation type
CPNE8	TF binding region
ENSG00000257718	TF binding region
ENSG00000163694	Chromatin interaction
ENSG00000124789	Chromatin interaction
ENSG00000120159	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10506128	1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10506130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1108123	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11170277	0.80[ASN][1000 genomes]
rs11829269	0.81[ASN][1000 genomes]
rs12305675	0.94[AMR][1000 genomes]
rs1684420	1.00[CEU][hapmap]
rs17126696	1.00[YRI][hapmap]
rs17126743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17126776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17126777	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4505102	0.88[ASN][1000 genomes]
rs57711782	0.82[ASN][1000 genomes]
rs58670318	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60914204	0.80[ASN][1000 genomes]
rs61628650	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr12:39296200-39300200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:39297000-39301200	Active TSS	Right Atrium	heart
3	chr12:39297200-39301000	Active TSS	Brain Hippocampus Middle	brain
4	chr12:39297200-39301000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:39297200-39301000	Active TSS	K562	blood
6	chr12:39297200-39301200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr12:39297400-39301000	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr12:39297600-39300800	Active TSS	Brain Anterior Caudate	brain
9	chr12:39297600-39301000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:39297600-39301400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:39297600-39301400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr12:39297800-39300200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:39297800-39301000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:39297800-39301200	Active TSS	Brain Angular Gyrus	brain
15	chr12:39297800-39301200	Active TSS	Brain Cingulate Gyrus	brain
16	chr12:39297800-39301400	Active TSS	GM12878-XiMat	blood
17	chr12:39298000-39300000	Active TSS	Osteobl	bone
18	chr12:39298000-39300200	Active TSS	NHLF	lung
19	chr12:39298000-39300800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr12:39298000-39300800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:39298000-39300800	Active TSS	Lung	lung
22	chr12:39298000-39301000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr12:39298000-39301000	Active TSS	Duodenum Mucosa	Duodenum
24	chr12:39298000-39301200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:39298000-39301400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:39298200-39299800	Active TSS	Stomach Smooth Muscle	stomach
27	chr12:39298200-39300000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:39298200-39300800	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr12:39298200-39300800	Active TSS	Rectal Smooth Muscle	rectum
30	chr12:39298200-39301000	Active TSS	Colon Smooth Muscle	Colon
31	chr12:39298200-39301000	Active TSS	Left Ventricle	heart
32	chr12:39298200-39301000	Active TSS	A549	lung
33	chr12:39298200-39301000	Active TSS	Hela-S3	cervix
34	chr12:39298200-39301200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr12:39298200-39301200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:39298200-39301200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr12:39298200-39301200	Active TSS	HMEC	breast
38	chr12:39298200-39301400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:39298200-39301400	Active TSS	Right Ventricle	heart
40	chr12:39298200-39301400	Active TSS	NHDF-Ad	bronchial
41	chr12:39298400-39300400	Active TSS	NHEK	skin
42	chr12:39298400-39300800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:39298400-39300800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:39298400-39300800	Active TSS	Liver	Liver
45	chr12:39298400-39300800	Active TSS	Esophagus	oesophagus
46	chr12:39298400-39301000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:39298400-39301000	Active TSS	H9 Cell Line	embryonic stem cell
48	chr12:39298400-39301000	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr12:39298400-39301000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:39298400-39301000	Active TSS	Primary T helper naive cells from peripheral blood	blood

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