Variant report

Variant	rs2242278
Chromosome Location	chr4:1165516-1165517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr4:1165491-1166425	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr4:1165160-1166154	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:1159180-1166648	PFSK-1	brain:	n/a	n/a
4	GABPA	chr4:1165511-1165943	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr4:1165380-1165530	GM12869	blood:	n/a	n/a
6	E2F6	chr4:1164540-1165835	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr4:1165380-1165530	GM12874	blood:	n/a	n/a
8	CTCF	chr4:1165400-1165550	BJ	skin:	n/a	n/a
9	POLR2A	chr4:1165041-1165790	PFSK-1	brain:	n/a	n/a
10	CTCF	chr4:1165460-1165610	GM12873	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1160471..1164177-chr4:1164804..1166602,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092535.1-1	chr4:1165314-1165862	NONHSAT094672

No data

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000273179	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1250125	0.81[TSI][hapmap]
rs1250126	0.80[MEX][hapmap];0.83[TSI][hapmap]
rs13118508	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17164380	0.86[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2242279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647932	1.00[YRI][hapmap]
rs4974633	0.83[EUR][1000 genomes]
rs62293562	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs652063	0.80[CHB][hapmap]
rs7700083	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking 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	40 gene(s)	inside rSNPs	diseases
4	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
5	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	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
8	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	nsv519106	chr4:1158991-1174861	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2242278	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs2242278	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs2242278	GAK	cis	cerebellum	SCAN
rs2242278	IDUA	cis	cerebellum	SCAN
rs2242278	RNF212	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1162000-1166200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:1163400-1165800	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:1164000-1166000	Transcr. at gene 5' and 3'	NHLF	lung
4	chr4:1164000-1167000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
5	chr4:1164200-1165600	Enhancers	Pancreas	Pancrea
6	chr4:1164200-1166400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:1164200-1167200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
8	chr4:1164400-1165800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:1164400-1166200	Bivalent Enhancer	Fetal Brain Male	brain
10	chr4:1164400-1167200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr4:1164600-1165600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:1164600-1165600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
13	chr4:1164600-1165600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
14	chr4:1164600-1165600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
15	chr4:1164600-1165800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr4:1164600-1166200	Flanking Active TSS	Right Ventricle	heart
17	chr4:1164600-1166400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:1164600-1166400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
19	chr4:1164600-1166600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
20	chr4:1164600-1166600	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr4:1164600-1166600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr4:1164600-1166800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:1164800-1165600	Enhancers	Primary hematopoietic stem cells	blood
24	chr4:1164800-1165600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:1164800-1165600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
26	chr4:1164800-1166600	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
27	chr4:1164800-1166600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:1164800-1166800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:1164800-1166800	Active TSS	NHDF-Ad	bronchial
30	chr4:1164800-1167000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr4:1165000-1165600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr4:1165000-1165600	Active TSS	Gastric	stomach
33	chr4:1165000-1165600	Bivalent/Poised TSS	Thymus	Thymus
34	chr4:1165000-1165800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:1165000-1165800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
36	chr4:1165000-1166000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr4:1165000-1166000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
38	chr4:1165000-1166000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
39	chr4:1165000-1166000	Weak transcription	Fetal Heart	heart
40	chr4:1165000-1166200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
41	chr4:1165000-1166400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr4:1165000-1166400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
43	chr4:1165000-1166400	Active TSS	Right Atrium	heart
44	chr4:1165000-1166600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr4:1165000-1166800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr4:1165000-1166800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr4:1165000-1167200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
48	chr4:1165200-1165600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:1165200-1165600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:1165200-1165600	Flanking Active TSS	Lung	lung

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