Variant report

Variant	rs1250089
Chromosome Location	chr4:1214487-1214488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1214372-1214690	K562	blood:	n/a	n/a
2	POLR2A	chr4:1214203-1214695	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr4:1214255-1214526	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr4:1214403-1214824	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:1214357-1214593	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:1214355-1214637	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:1214365-1214609	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:1214454-1214504	HUVEC	blood vessel:	n/a
2	chr4:1214454-1214504	U87	brain:	n/a
3	chr4:1214454-1214504	HNPCEpiC	eye:	n/a
4	chr4:1214454-1214504	HCM	heart:	n/a
5	chr4:1214454-1214504	MCF-7	breast:	n/a
6	chr4:1214454-1214504	HCPEpiC	choroid plexus:	n/a
7	chr4:1214454-1214504	Hela-S3	cervix:	n/a
8	chr4:1214454-1214504	Caco-2	colon:	n/a
9	chr4:1214454-1214504	NHDF-neo	bronchial:	n/a
10	chr4:1214454-1214504	AG04450	lung:	fetal
11	chr4:1214454-1214504	HRCEpiC	kidney:	n/a
12	chr4:1214454-1214504	HRPEpiC	eye:	n/a
13	chr4:1214454-1214504	HepG2	liver:	n/a
14	chr4:1214454-1214504	GM12892	blood:	n/a
15	chr4:1214454-1214504	RPTEC	kidney:	n/a
16	chr4:1214454-1214504	SAEC	small airway:	n/a
17	chr4:1214454-1214504	HRE	kidney:	n/a
18	chr4:1214454-1214504	HAEpiC	amniotic membrane:	n/a
19	chr4:1214454-1214504	PANC-1	pancreas:	n/a
20	chr4:1214454-1214504	NB4	blood:	n/a
21	chr4:1214454-1214504	BJ	skin:	n/a
22	chr4:1214454-1214504	NHBE	bronchial:	n/a
23	chr4:1214454-1214504	AG09319	gingival:	n/a
24	chr4:1214454-1214504	LNCaP	prostate:	n/a
25	chr4:1214454-1214504	AG04449	skin:	fetal
26	chr4:1214454-1214504	GM06990	blood:	n/a
27	chr4:1214454-1214504	GM19239	blood:	n/a
28	chr4:1214454-1214504	HMEC	breast:	n/a
29	chr4:1214454-1214504	HEK293	kidney:	embryo
30	chr4:1214454-1214504	SK-N-SH_RA	brain:	n/a
31	chr4:1214454-1214504	SKMC	muscle:	n/a
32	chr4:1214454-1214504	ProgFib	skin:	n/a
33	chr4:1214454-1214504	HL-60	blood:	n/a
34	chr4:1214454-1214504	SK-N-SH	brain:	n/a
35	chr4:1214454-1214504	BE2_C	brain:	n/a
36	chr4:1214454-1214504	ovcar-3	ovarian:	n/a
37	chr4:1214454-1214504	CMK	blood:	n/a
38	chr4:1214454-1214504	SK-N-MC	brain:	n/a
39	chr4:1214454-1214504	MCF10A-Er-Src	breast:	n/a
40	chr4:1214454-1214504	PrEC	prostate:	n/a
41	chr4:1214454-1214504	AoSMC	blood vessel:	n/a
42	chr4:1214454-1214504	PFSK-1	brain:	n/a
43	chr4:1214454-1214504	HPAEpiC	pulmonary alveolar:	n/a
44	chr4:1214454-1214504	GM12891	blood:	n/a
45	chr4:1214454-1214504	A549	lung:	n/a
46	chr4:1214454-1214504	NH-A	brain:	n/a
47	chr4:1214454-1214504	AG09309	skin:	n/a
48	chr4:1214454-1214504	IMR90	lung:	fetal
49	chr4:1214454-1214504	T-47D	breast:	n/a
50	chr4:1214454-1214504	HEEpiC	esophagus:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1213244..1216173-chr4:1340937..1342611,2	MCF-7	breast:
2	chr4:1213077..1214690-chr4:1242056..1244324,2	K562	blood:
3	chr4:1213778..1216282-chr4:1220855..1223154,2	MCF-7	breast:

No data

Variant related genes	Relation type
CTBP1	TF binding region
CTBP1	CpG island
ENSG00000163945	Chromatin interaction
ENSG00000196810	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1250091	0.80[EUR][1000 genomes]
rs1250092	0.92[EUR][1000 genomes]
rs1250105	0.90[EUR][1000 genomes]
rs1250106	0.86[EUR][1000 genomes]
rs1250108	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1250118	0.90[EUR][1000 genomes]
rs1680056	0.93[EUR][1000 genomes]
rs2306475	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35376712	0.91[EUR][1000 genomes]
rs4993865	0.91[EUR][1000 genomes]
rs6821834	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	nsv1002097	chr4:1212573-1320086	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
25	nsv536986	chr4:1212573-1320086	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1250089	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs1250089	CTBP1	Cis_1M	lymphoblastoid	RTeQTL

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	chr4:1202800-1218000	Weak transcription	Fetal Brain Male	brain
3	chr4:1203200-1217800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:1203800-1223000	Strong transcription	Osteobl	bone
5	chr4:1204000-1218000	Weak transcription	K562	blood
6	chr4:1204400-1227200	Strong transcription	Fetal Intestine Small	intestine
7	chr4:1204400-1235800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:1204600-1220400	Strong transcription	Liver	Liver
9	chr4:1204600-1236200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:1204800-1226400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:1204800-1237000	Weak transcription	Psoas Muscle	Psoas
12	chr4:1205000-1226200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:1205200-1218000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:1205400-1226800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:1205800-1228200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:1206000-1226800	Strong transcription	Fetal Brain Female	brain
17	chr4:1206400-1226800	Strong transcription	Brain Germinal Matrix	brain
18	chr4:1206600-1227600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:1207600-1218200	Weak transcription	Hela-S3	cervix
20	chr4:1208800-1228000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr4:1209000-1218000	Weak transcription	Stomach Mucosa	stomach
22	chr4:1209400-1215000	Weak transcription	Ovary	ovary
23	chr4:1209800-1215400	Weak transcription	HSMMtube	muscle
24	chr4:1209800-1218000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:1210400-1214600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:1210400-1214600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:1210400-1215000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:1210600-1225200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:1210800-1215400	Weak transcription	Brain Substantia Nigra	brain
30	chr4:1210800-1217800	Weak transcription	Fetal Heart	heart
31	chr4:1210800-1218000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:1211000-1217800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:1211200-1214600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:1211200-1215000	Weak transcription	Colonic Mucosa	Colon
35	chr4:1211200-1215000	Strong transcription	Fetal Intestine Large	intestine
36	chr4:1211200-1217800	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:1211400-1215200	Weak transcription	Left Ventricle	heart
38	chr4:1211400-1216600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:1211400-1219600	Weak transcription	Right Atrium	heart
40	chr4:1211400-1235400	Weak transcription	Small Intestine	intestine
41	chr4:1211600-1215000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:1211600-1215400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:1211600-1215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:1211600-1215800	Weak transcription	Right Ventricle	heart
45	chr4:1211600-1217000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:1211600-1217200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:1211600-1217600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:1211600-1235400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:1211800-1214800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr4:1211800-1215000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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