Variant report

Variant	rs11168975
Chromosome Location	chr12:49716782-49716783
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	SRF	chr12:49716447-49717334	MCF-7	breast:	n/a	n/a
2	RCOR1	chr12:49716553-49717230	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:49716455-49716886	A549	lung:	n/a	n/a
4	POLR2A	chr12:49715570-49717849	K562	blood:	n/a	n/a
5	TAF1	chr12:49716511-49716829	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr12:49716514-49717329	GM12878	blood:	n/a	n/a
7	PAX5	chr12:49716589-49717063	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:49715738-49717250	GM12878	blood:	n/a	n/a
9	SP2	chr12:49716675-49717172	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:49716093-49717368	PANC-1	pancreas:	n/a	n/a
11	E2F6	chr12:49716517-49717114	K562	blood:	n/a	chr12:49716850-49716859 chr12:49716847-49716859 chr12:49717018-49717027
12	POLR2A	chr12:49716555-49716861	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:49716497-49716911	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOXM1	chr12:49715720-49717357	GM12878	blood:	n/a	n/a
15	HA-E2F1	chr12:49716468-49717333	MCF-7	breast:	n/a	chr12:49716850-49716859 chr12:49717258-49717268 chr12:49716847-49716859 chr12:49717018-49717027
16	E2F4	chr12:49716561-49717827	K562	blood:	n/a	chr12:49716850-49716859 chr12:49717258-49717268 chr12:49716847-49716859 chr12:49717018-49717027
17	YY1	chr12:49716445-49717234	HepG2	liver:	n/a	n/a
18	ZBTB33	chr12:49716480-49717352	A549	lung:	n/a	chr12:49716785-49716795 chr12:49716788-49716798
19	POLR2A	chr12:49716445-49717255	H1-neurons	neurons:	n/a	n/a
20	ELF1	chr12:49716453-49717207	GM12878	blood:	n/a	chr12:49716993-49717005
21	TAF1	chr12:49716512-49717259	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr12:49716534-49717290	GM12878	blood:	n/a	n/a
23	ELF1	chr12:49716601-49717259	K562	blood:	n/a	chr12:49716993-49717005
24	POLR2A	chr12:49715661-49717299	K562	blood:	n/a	n/a
25	TCF12	chr12:49716331-49717629	ECC-1	luminal epithelium:	n/a	n/a
26	CREB1	chr12:49716659-49717216	H1-hESC	embryonic stem cell:	n/a	n/a
27	IRF3	chr12:49716760-49717122	GM12878	blood:	n/a	chr12:49716846-49716860
28	ZBTB33	chr12:49716505-49717317	GM12878	blood:	n/a	chr12:49716785-49716795 chr12:49716788-49716798
29	POLR2A	chr12:49716332-49717375	GM12878	blood:	n/a	n/a
30	YY1	chr12:49716600-49716830	A549	lung:	n/a	n/a
31	POLR2A	chr12:49715650-49717321	ECC-1	luminal epithelium:	n/a	n/a
32	TAF1	chr12:49716011-49717533	ECC-1	luminal epithelium:	n/a	n/a
33	BHLHE40	chr12:49716654-49717148	K562	blood:	n/a	n/a
34	POLR2A	chr12:49716512-49716850	H1-hESC	embryonic stem cell:	n/a	n/a
35	TAF1	chr12:49716588-49717199	SK-N-SH	brain:	n/a	n/a
36	SP1	chr12:49716755-49717187	H1-hESC	embryonic stem cell:	n/a	chr12:49716849-49716858 chr12:49716849-49716863 chr12:49716850-49716859 chr12:49716867-49716888
37	SP1	chr12:49716611-49717225	GM12878	blood:	n/a	chr12:49716849-49716858 chr12:49716849-49716863 chr12:49716850-49716859 chr12:49716867-49716888
38	GTF2F1	chr12:49716513-49717165	Hela-S3	cervix:	n/a	n/a
39	TBP	chr12:49716647-49717214	Hela-S3	cervix:	n/a	n/a
40	CREB1	chr12:49716413-49717254	A549	lung:	n/a	n/a
41	POLR2A	chr12:49715718-49717395	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:49716500-49717309	GM18526	blood:	n/a	n/a
43	MXI1	chr12:49716157-49717612	IMR90	lung:	n/a	n/a
44	SP1	chr12:49716594-49717207	H1-hESC	embryonic stem cell:	n/a	chr12:49716849-49716858 chr12:49716849-49716863 chr12:49716850-49716859 chr12:49716867-49716888
45	TBP	chr12:49716602-49717203	GM12878	blood:	n/a	n/a
46	E2F4	chr12:49716589-49718006	Hela-S3	cervix:	n/a	chr12:49716850-49716859 chr12:49717258-49717268 chr12:49716847-49716859 chr12:49717018-49717027
47	BRCA1	chr12:49716598-49717144	H1-hESC	embryonic stem cell:	n/a	chr12:49716787-49716796
48	MXI1	chr12:49715742-49717647	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr12:49716562-49716860	HepG2	liver:	n/a	n/a
50	GATA2	chr12:49716039-49717278	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49716418..49717227-chr15:52861024..52861524,2	NB4	blood:
2	chr12:49716225..49717888-chr12:49960972..49962551,2	K562	blood:
3	chr12:49715203..49717456-chr12:49729386..49731841,3	MCF-7	breast:
4	chr12:49715809..49718434-chr12:49958773..49962472,3	K562	blood:
5	chr12:49684454..49687869-chr12:49714567..49717463,3	K562	blood:
6	chr12:49715364..49717044-chr12:50101181..50102827,2	K562	blood:
7	chr12:49657208..49661363-chr12:49714955..49717990,5	MCF-7	breast:
8	chr12:49689988..49692308-chr12:49713640..49717456,5	K562	blood:
9	chr12:49685018..49687263-chr12:49715369..49717175,2	K562	blood:
10	chr12:49657692..49659587-chr12:49716247..49718208,2	MCF-7	breast:
11	chr12:49686580..49692358-chr12:49712251..49718367,13	MCF-7	breast:
12	chr12:49715312..49722303-chr12:49739075..49744198,13	MCF-7	breast:
13	chr12:49657320..49660807-chr12:49714613..49719662,6	K562	blood:
14	chr12:49658775..49661727-chr12:49715622..49718429,2	K562	blood:
15	chr12:49716623..49719210-chr12:49759055..49761901,3	MCF-7	breast:
16	chr11:62608481..62608987-chr12:49716348..49716882,2	Hela-S3	cervix:

Variant related genes	Relation type
TROAP	TF binding region
ENSG00000167553	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000161791	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000187778	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10400435	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.92[ASN][1000 genomes]
rs10400567	0.92[ASN][1000 genomes]
rs10875948	1.00[JPT][hapmap]
rs11168967	1.00[JPT][hapmap]
rs11168973	0.96[ASN][1000 genomes]
rs11168974	1.00[ASN][1000 genomes]
rs11168981	0.82[CHB][hapmap]
rs11503617	0.96[ASN][1000 genomes]
rs11835037	1.00[JPT][hapmap]
rs11835303	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11837234	1.00[JPT][hapmap]
rs12306866	0.82[CHB][hapmap]
rs12313488	0.96[ASN][1000 genomes]
rs12318618	1.00[JPT][hapmap]
rs12322335	1.00[JPT][hapmap]
rs12580931	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12581428	1.00[JPT][hapmap]
rs12822293	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs2070760	0.92[ASN][1000 genomes]
rs2236746	1.00[JPT][hapmap]
rs2270741	0.82[CHB][hapmap]
rs28493849	0.92[ASN][1000 genomes]
rs3088008	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4243545	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[ASN][1000 genomes]
rs4898504	0.96[ASN][1000 genomes]
rs4898519	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs57241318	1.00[ASN][1000 genomes]
rs59575791	0.96[ASN][1000 genomes]
rs67236923	0.92[ASN][1000 genomes]
rs67309388	0.92[ASN][1000 genomes]
rs7295247	1.00[JPT][hapmap]
rs7299812	0.82[CHB][hapmap]
rs73112143	0.92[ASN][1000 genomes]
rs73309977	0.96[ASN][1000 genomes]
rs7342318	1.00[JPT][hapmap]
rs7342384	1.00[JPT][hapmap]
rs7488343	0.92[ASN][1000 genomes]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11168975	TMEM117	cis	cerebellum	SCAN
rs11168975	PRPH	cis	cerebellum	SCAN
rs11168975	C1QL4	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49715600-49717000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:49715600-49717600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:49715800-49717200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:49715800-49717600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr12:49715800-49717600	Active TSS	HSMMtube	muscle
6	chr12:49715800-49717600	Active TSS	K562	blood
7	chr12:49715800-49717800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:49715800-49717800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr12:49715800-49718200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:49715800-49718200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr12:49716000-49717200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:49716000-49717200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:49716000-49717200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr12:49716000-49717200	Active TSS	Colonic Mucosa	Colon
15	chr12:49716000-49717200	Active TSS	Colon Smooth Muscle	Colon
16	chr12:49716000-49717400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:49716000-49717400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:49716000-49717400	Active TSS	Brain Substantia Nigra	brain
19	chr12:49716000-49717400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr12:49716000-49717400	Active TSS	Fetal Intestine Large	intestine
21	chr12:49716000-49717400	Active TSS	HSMM	muscle
22	chr12:49716000-49717800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr12:49716000-49718000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr12:49716200-49716800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:49716200-49717200	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr12:49716200-49717200	Active TSS	Aorta	Aorta
27	chr12:49716200-49717200	Active TSS	Brain Anterior Caudate	brain
28	chr12:49716200-49717200	Active TSS	Brain Hippocampus Middle	brain
29	chr12:49716200-49717200	Active TSS	Esophagus	oesophagus
30	chr12:49716200-49717200	Active TSS	Gastric	stomach
31	chr12:49716200-49717200	Active TSS	Right Atrium	heart
32	chr12:49716200-49717200	Active TSS	Right Ventricle	heart
33	chr12:49716200-49717400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:49716200-49717400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr12:49716200-49717400	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr12:49716200-49717400	Active TSS	Psoas Muscle	Psoas
37	chr12:49716200-49717400	Active TSS	A549	lung
38	chr12:49716200-49717600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:49716200-49717600	Active TSS	Brain Angular Gyrus	brain
40	chr12:49716200-49717600	Active TSS	Small Intestine	intestine
41	chr12:49716200-49717800	Active TSS	Fetal Kidney	kidney
42	chr12:49716200-49718000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:49716200-49718000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr12:49716200-49718000	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr12:49716200-49718000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr12:49716200-49718000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:49716400-49717000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:49716400-49717000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:49716400-49717000	Active TSS	Duodenum Mucosa	Duodenum
50	chr12:49716400-49717000	Active TSS	Fetal Brain Male	brain

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