Variant report

Variant	rs12508446
Chromosome Location	chr4:1198957-1198958
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	MXI1	chr4:1198287-1199229	HepG2	liver:	n/a	n/a
2	MYC	chr4:1198886-1199038	MCF-7	breast:	n/a	n/a
3	USF1	chr4:1198802-1199084	HepG2	liver:	n/a	n/a
4	MYBL2	chr4:1198602-1199273	HepG2	liver:	n/a	n/a
5	NFIC	chr4:1198605-1199084	HepG2	liver:	n/a	n/a
6	RAD21	chr4:1198757-1199152	HepG2	liver:	n/a	chr4:1198984-1198997 chr4:1198991-1199001 chr4:1199079-1199098
7	POLR2A	chr4:1197694-1199659	HepG2	liver:	n/a	n/a
8	MAX	chr4:1198145-1199386	HepG2	liver:	n/a	n/a
9	HNF4A	chr4:1198766-1199406	HepG2	liver:	n/a	n/a
10	SP1	chr4:1198695-1199283	HepG2	liver:	n/a	chr4:1198944-1198954 chr4:1198944-1198954 chr4:1199180-1199189
11	TEAD4	chr4:1198532-1199107	HepG2	liver:	n/a	n/a
12	MAX	chr4:1198380-1199345	HepG2	liver:	n/a	n/a
13	TAF1	chr4:1198659-1199239	HepG2	liver:	n/a	n/a
14	YY1	chr4:1198712-1199331	HepG2	liver:	n/a	n/a
15	HNF4G	chr4:1198772-1199183	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:1198649-1199252	HepG2	liver:	n/a	n/a
17	MYBL2	chr4:1198517-1199265	HepG2	liver:	n/a	n/a
18	MAFF	chr4:1198817-1199055	HepG2	liver:	n/a	n/a
19	SMC3	chr4:1198692-1199124	HepG2	liver:	n/a	n/a
20	HDAC2	chr4:1198686-1199191	HepG2	liver:	n/a	n/a
21	MYC	chr4:1198919-1199009	MCF-7	breast:	n/a	n/a
22	POLR2A	chr4:1198655-1199190	HepG2	liver:	n/a	n/a
23	POLR2A	chr4:1198702-1199192	HepG2	liver:	n/a	n/a
24	SIN3AK20	chr4:1198761-1199116	HepG2	liver:	n/a	n/a
25	POLR2A	chr4:1198587-1199273	HepG2	liver:	n/a	n/a
26	TAF1	chr4:1198681-1199215	HepG2	liver:	n/a	n/a
27	MBD4	chr4:1198571-1199147	HepG2	liver:	n/a	n/a
28	USF1	chr4:1198909-1199069	HepG2	liver:	n/a	n/a
29	MAX	chr4:1198034-1199420	HepG2	liver:	n/a	n/a
30	RAD21	chr4:1198801-1199222	HepG2	liver:	n/a	chr4:1198984-1198997 chr4:1198991-1199001 chr4:1199079-1199098
31	RFX5	chr4:1198844-1199074	HepG2	liver:	n/a	n/a
32	POLR2A	chr4:1198693-1199271	HepG2	liver:	n/a	n/a
33	CEBPD	chr4:1198632-1199154	HepG2	liver:	n/a	n/a
34	ELF1	chr4:1198731-1199109	HepG2	liver:	n/a	n/a
35	RXRA	chr4:1198815-1199127	HepG2	liver:	n/a	chr4:1199048-1199062
36	HNF4G	chr4:1198757-1199319	HepG2	liver:	n/a	n/a
37	HEY1	chr4:1198545-1199333	HepG2	liver:	n/a	n/a
38	HNF4A	chr4:1198709-1199224	HepG2	liver:	n/a	n/a
39	SIN3AK20	chr4:1198680-1199108	HepG2	liver:	n/a	n/a
40	ELF1	chr4:1198641-1199210	HepG2	liver:	n/a	n/a
41	JUND	chr4:1198789-1199083	HepG2	liver:	n/a	n/a
42	EP300	chr4:1198714-1199112	HepG2	liver:	n/a	n/a
43	POLR2A	chr4:1198752-1199177	HepG2	liver:	n/a	n/a
44	ZBTB7A	chr4:1198886-1199076	HepG2	liver:	n/a	n/a
45	MAFK	chr4:1198698-1199099	HepG2	liver:	n/a	chr4:1198714-1198728
46	EP300	chr4:1198421-1199517	SK-N-SH	brain:	n/a	chr4:1199151-1199167
47	HNF4A	chr4:1198798-1199195	HepG2	liver:	n/a	n/a
48	MAZ	chr4:1198833-1199439	HepG2	liver:	n/a	n/a
49	MYC	chr4:1198767-1199194	HepG2	liver:	n/a	n/a
50	REST	chr4:1198648-1199156	HepG2	liver:	n/a	chr4:1199030-1199040

No.	Distal block	Cell Line	Cell type
1	chr4:1198351..1202176-chr4:1203916..1208029,5	K562	blood:
2	chr4:1192255..1195518-chr4:1197581..1201308,4	MCF-7	breast:
3	chr4:1198322..1201004-chr4:1242228..1244589,3	K562	blood:

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000159674	Chromatin interaction
ENSG00000196810	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11247983	0.92[CEU][hapmap]
rs11721789	0.88[CEU][hapmap]
rs11727167	0.92[CEU][hapmap]
rs12499546	0.88[CEU][hapmap]
rs12502916	0.92[CEU][hapmap]
rs12641735	0.85[CEU][hapmap]
rs12642410	0.92[CEU][hapmap]
rs13110563	0.88[CEU][hapmap]
rs13112706	0.92[CEU][hapmap]
rs13128045	0.92[CEU][hapmap]
rs13134106	0.92[CEU][hapmap]
rs13149575	0.92[CEU][hapmap]
rs13149952	0.92[CEU][hapmap]
rs13150571	0.92[CEU][hapmap]
rs1316393	0.88[CEU][hapmap]
rs1564508	0.88[CEU][hapmap]
rs1680073	0.85[CEU][hapmap]
rs1680074	0.85[CEU][hapmap]
rs1732100	0.85[CEU][hapmap]
rs1732107	0.92[CEU][hapmap]
rs1960426	0.88[CEU][hapmap]
rs2199956	0.84[CEU][hapmap]
rs2279281	0.88[CEU][hapmap]
rs2291199	0.88[CEU][hapmap]
rs2335855	0.88[CEU][hapmap]
rs34490749	0.81[EUR][1000 genomes]
rs3755920	0.84[CEU][hapmap]
rs3775099	0.81[CEU][hapmap]
rs3894353	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3915420	0.88[CEU][hapmap]
rs4045131	0.80[CEU][hapmap]
rs4246685	0.92[CEU][hapmap]
rs4405964	0.92[CEU][hapmap]
rs4428235	0.92[CEU][hapmap]
rs4493483	0.92[CEU][hapmap]
rs4516656	0.92[CEU][hapmap]
rs4519749	0.92[CEU][hapmap]
rs4642180	0.92[CEU][hapmap]
rs4974540	0.81[EUR][1000 genomes]
rs4974574	0.80[CEU][hapmap]
rs4974582	0.95[CEU][hapmap]
rs4974594	0.84[CEU][hapmap]
rs7673398	0.84[CEU][hapmap]
rs7695691	0.84[CEU][hapmap]
rs900027	0.92[CEU][hapmap]
rs900028	0.92[CEU][hapmap]
rs922698	0.84[CEU][hapmap]
rs9631804	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
7	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	71 gene(s)	inside rSNPs	diseases
9	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
14	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
15	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
16	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
17	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
21	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12508446	MAEA	cis	Nerve Tibial	GTEx
rs12508446	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs12508446	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs12508446	CTBP1	cis	multi-tissue	Pritchard
rs12508446	UVSSA	cis	Whole Blood	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1185000-1204200	Enhancers	Fetal Muscle Leg	muscle
2	chr4:1194200-1207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:1194600-1201600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:1194600-1202400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:1194800-1199600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:1194800-1200400	Weak transcription	Ovary	ovary
7	chr4:1194800-1201400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:1194800-1201800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:1194800-1201800	Weak transcription	Osteobl	bone
10	chr4:1194800-1202000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:1194800-1203000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:1194800-1203400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:1195000-1201400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:1195000-1201600	Weak transcription	Right Atrium	heart
15	chr4:1195200-1200000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:1195200-1200600	Weak transcription	Pancreas	Pancrea
17	chr4:1195200-1201200	Enhancers	Spleen	Spleen
18	chr4:1195200-1201400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:1195200-1201600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:1195200-1201600	Weak transcription	Right Ventricle	heart
21	chr4:1195200-1202600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:1195200-1204400	Weak transcription	HMEC	breast
23	chr4:1195200-1214600	Weak transcription	A549	lung
24	chr4:1195400-1199600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:1195800-1201000	Weak transcription	Fetal Brain Female	brain
26	chr4:1196000-1199000	Enhancers	Primary B cells from peripheral blood	blood
27	chr4:1196400-1199200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr4:1196400-1200800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:1196400-1201600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:1196400-1203000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:1196400-1203200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr4:1196400-1209800	Weak transcription	Primary B cells from cord blood	blood
33	chr4:1196600-1202400	Weak transcription	NH-A	brain
34	chr4:1196600-1202600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr4:1196800-1200600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr4:1196800-1201400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:1196800-1201400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:1196800-1201600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:1196800-1202400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:1196800-1204200	Enhancers	Placenta	Placenta
41	chr4:1196800-1204400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr4:1197000-1201600	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:1197000-1203000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:1197000-1204400	Enhancers	Fetal Muscle Trunk	muscle
45	chr4:1197200-1200600	Weak transcription	Esophagus	oesophagus
46	chr4:1197200-1201800	Weak transcription	Thymus	Thymus
47	chr4:1197400-1199000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr4:1197400-1199200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:1197400-1203200	Weak transcription	Primary T cells from cord blood	blood
50	chr4:1197600-1200400	Weak transcription	Brain Germinal Matrix	brain

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