Variant report

Variant	rs1250092
Chromosome Location	chr4:1210654-1210655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:1210620-1210770	GM12869	blood:	n/a	n/a
2	POLR2A	chr4:1209933-1210945	GM12892	blood:	n/a	n/a
3	FOXM1	chr4:1210536-1210942	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:1209574-1211350	HL-60	blood:	n/a	n/a
5	CTCF	chr4:1210620-1210870	GM12801	blood:	n/a	n/a
6	POLR2A	chr4:1209548-1211003	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:1209534-1210709	K562	blood:	n/a	n/a
8	SPI1	chr4:1210490-1211074	HL-60	blood:	n/a	n/a
9	CTCF	chr4:1210635-1210656	GM10248	blood:	n/a	n/a
10	POLR2A	chr4:1208736-1211035	GM12892	blood:	n/a	n/a
11	RUNX3	chr4:1210495-1211003	GM12878	blood:	n/a	n/a
12	MTA3	chr4:1208835-1211238	GM12878	blood:	n/a	n/a
13	EBF1	chr4:1210586-1210942	GM12878	blood:	n/a	n/a
14	YY1	chr4:1210539-1210747	GM12878	blood:	n/a	n/a
15	TCF3	chr4:1210447-1210799	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:1210526-1210685	GM12878	blood:	n/a	n/a
17	ELF1	chr4:1208687-1211263	GM12878	blood:	n/a	n/a
18	SPI1	chr4:1210593-1210924	GM12878	blood:	n/a	n/a
19	EGR1	chr4:1210646-1210856	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:1210515-1211023	GM12892	blood:	n/a	n/a
21	SPI1	chr4:1210630-1210930	HL-60	blood:	n/a	n/a
22	POLR2A	chr4:1209599-1210782	HepG2	liver:	n/a	n/a
23	SPI1	chr4:1210588-1210863	GM12891	blood:	n/a	n/a
24	CTCF	chr4:1210560-1210830	GM12869	blood:	n/a	n/a
25	POLR2A	chr4:1208835-1211179	GM12878	blood:	n/a	n/a
26	RUNX3	chr4:1210530-1211062	GM12878	blood:	n/a	n/a
27	NFIC	chr4:1210588-1210981	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1209494..1211546-chr4:1218177..1220594,3	MCF-7	breast:
2	chr4:1210359..1211936-chr4:1235947..1237642,2	K562	blood:
3	chr4:1203383..1207466-chr4:1208474..1210757,3	K562	blood:
4	chr4:1210297..1212921-chr4:1219688..1223007,3	K562	blood:
5	chr2:86422281..86424225-chr4:1209194..1210696,2	K562	blood:

No data

Variant related genes	Relation type
CTBP1	TF binding region
ENSG00000159692	Chromatin interaction
ENSG00000132305	Chromatin interaction
ENSG00000273080	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1250088	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1250089	0.92[EUR][1000 genomes]
rs1250091	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1250105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1250106	0.93[EUR][1000 genomes]
rs1250108	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1250118	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1250126	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1265922	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1680030	0.80[CEU][hapmap]
rs1680056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306475	0.91[EUR][1000 genomes]
rs35376712	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4993865	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821834	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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
22	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
23	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
24	nsv966246	chr4:1205017-1210824	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
25	esv3436317	chr4:1208602-1211100	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
26	esv3355881	chr4:1209202-1211700	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1250092	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs1250092	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs1250092	UVSSA	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1195200-1214600	Weak transcription	A549	lung
2	chr4:1198000-1211200	Genic enhancers	Fetal Stomach	stomach
3	chr4:1201600-1211600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:1202800-1218000	Weak transcription	Fetal Brain Male	brain
5	chr4:1203200-1217800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:1203400-1213000	Weak transcription	Fetal Kidney	kidney
7	chr4:1203800-1223000	Strong transcription	Osteobl	bone
8	chr4:1204000-1211600	Genic enhancers	Esophagus	oesophagus
9	chr4:1204000-1218000	Weak transcription	K562	blood
10	chr4:1204200-1212600	Genic enhancers	Fetal Muscle Leg	muscle
11	chr4:1204400-1210800	Strong transcription	Fetal Intestine Large	intestine
12	chr4:1204400-1211600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:1204400-1211600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:1204400-1211600	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr4:1204400-1212000	Strong transcription	NHEK	skin
16	chr4:1204400-1227200	Strong transcription	Fetal Intestine Small	intestine
17	chr4:1204400-1235800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:1204600-1220400	Strong transcription	Liver	Liver
19	chr4:1204600-1236200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:1204800-1211000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:1204800-1212000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr4:1204800-1213800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:1204800-1226400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:1204800-1237000	Weak transcription	Psoas Muscle	Psoas
25	chr4:1205000-1211000	Weak transcription	Right Atrium	heart
26	chr4:1205000-1213400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:1205000-1226200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:1205200-1211800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:1205200-1218000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:1205400-1226800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:1205800-1211400	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr4:1205800-1211600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:1205800-1228200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:1206000-1211600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr4:1206000-1212000	Strong transcription	Colon Smooth Muscle	Colon
36	chr4:1206000-1226800	Strong transcription	Fetal Brain Female	brain
37	chr4:1206200-1211400	Strong transcription	Aorta	Aorta
38	chr4:1206400-1210800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:1206400-1226800	Strong transcription	Brain Germinal Matrix	brain
40	chr4:1206600-1210800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr4:1206600-1210800	Genic enhancers	Spleen	Spleen
42	chr4:1206600-1227600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:1206800-1212600	Weak transcription	NHDF-Ad	bronchial
44	chr4:1207200-1213600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:1207600-1218200	Weak transcription	Hela-S3	cervix
46	chr4:1208000-1211600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr4:1208200-1211200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr4:1208400-1212600	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr4:1208600-1213400	Strong transcription	HepG2	liver
50	chr4:1208800-1211200	Strong transcription	HMEC	breast

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