Variant report

Variant	rs1250106
Chromosome Location	chr4:1202024-1202025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1201408-1202093	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr4:1201797-1202187	U87	brain:	n/a	n/a
3	POLR2A	chr4:1201720-1203300	U87	brain:	n/a	n/a
4	POLR2A	chr4:1201702-1202079	PANC-1	pancreas:	n/a	n/a
5	RCOR1	chr4:1201473-1202198	IMR90	lung:	n/a	n/a
6	TCF7L2	chr4:1201708-1202078	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr4:1201804-1203215	SK-N-MC	brain:	n/a	n/a
8	MAZ	chr4:1201469-1203117	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:1201438..1204113-chr4:1239051..1243365,5	MCF-7	breast:
2	chr4:1198351..1202176-chr4:1203916..1208029,5	K562	blood:
3	chr4:1199021..1202194-chr4:1205945..1209496,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092535.1-1	chr4:1201668-1202165	NONHSAT094683
2	lnc-AC092535.1-1	chr4:1201668-1202155	NONHSAT094674

No data

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

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1250089	0.86[EUR][1000 genomes]
rs1250091	0.81[EUR][1000 genomes]
rs1250092	0.93[EUR][1000 genomes]
rs1250103	0.90[ASN][1000 genomes]
rs1250105	0.93[EUR][1000 genomes]
rs1250108	0.84[EUR][1000 genomes]
rs1250118	0.93[EUR][1000 genomes]
rs1680056	0.94[EUR][1000 genomes]
rs2306475	0.87[EUR][1000 genomes]
rs35376712	0.91[EUR][1000 genomes]
rs4993865	0.94[EUR][1000 genomes]
rs6821834	0.90[EUR][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1250106	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs1250106	UVSSA	cis	Whole Blood	GTEx
rs1250106	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs1250106	CTBP1	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

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	chr4:1194600-1202400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr4:1194800-1203000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:1194800-1203400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:1195200-1202600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:1195200-1204400	Weak transcription	HMEC	breast
8	chr4:1195200-1214600	Weak transcription	A549	lung
9	chr4:1196400-1203000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:1196400-1203200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr4:1196400-1209800	Weak transcription	Primary B cells from cord blood	blood
12	chr4:1196600-1202400	Weak transcription	NH-A	brain
13	chr4:1196600-1202600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr4:1196800-1202400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:1196800-1204200	Enhancers	Placenta	Placenta
16	chr4:1196800-1204400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:1197000-1203000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:1197000-1204400	Enhancers	Fetal Muscle Trunk	muscle
19	chr4:1197400-1203200	Weak transcription	Primary T cells from cord blood	blood
20	chr4:1197600-1202400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:1197600-1202800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr4:1197600-1203000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:1197600-1204400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:1197600-1204600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:1198000-1211200	Genic enhancers	Fetal Stomach	stomach
26	chr4:1198200-1205200	Enhancers	Stomach Mucosa	stomach
27	chr4:1198400-1202200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:1198400-1204000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:1198400-1204400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:1198400-1204600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:1198400-1207000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:1198600-1202400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:1198600-1204800	Weak transcription	GM12878-XiMat	blood
34	chr4:1198800-1202200	Enhancers	Adipose Nuclei	Adipose
35	chr4:1199000-1202200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr4:1199000-1202200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:1199000-1204200	Weak transcription	Dnd41	blood
38	chr4:1199000-1205800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:1199200-1202200	Enhancers	Colonic Mucosa	Colon
40	chr4:1199200-1202200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr4:1199200-1202600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:1199200-1207600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:1199400-1202400	Enhancers	Fetal Intestine Large	intestine
44	chr4:1200000-1203000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:1200000-1205200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:1200200-1204600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:1200400-1206200	Enhancers	Ovary	ovary
48	chr4:1200400-1206400	Genic enhancers	Brain Germinal Matrix	brain
49	chr4:1200600-1202200	Enhancers	Esophagus	oesophagus
50	chr4:1200600-1204800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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