Variant report

Variant	rs1250103
Chromosome Location	chr4:1197552-1197553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF4	chr4:1197243-1197680	GM12878	blood:	n/a	n/a
2	TCF12	chr4:1197290-1197621	GM12878	blood:	n/a	n/a
3	EBF1	chr4:1197323-1197659	GM12878	blood:	n/a	chr4:1197571-1197582
4	POU2F2	chr4:1197237-1197806	GM12878	blood:	n/a	n/a
5	BATF	chr4:1197359-1197602	GM12878	blood:	n/a	n/a
6	MTA3	chr4:1197229-1197792	GM12878	blood:	n/a	n/a
7	POU2F2	chr4:1197424-1197669	GM12878	blood:	n/a	n/a
8	NFIC	chr4:1197298-1197648	GM12878	blood:	n/a	n/a
9	YY1	chr4:1197320-1197637	GM12878	blood:	n/a	n/a
10	MAX	chr4:1197187-1197712	GM12878	blood:	n/a	n/a
11	PAX5	chr4:1197333-1197652	GM12878	blood:	n/a	n/a
12	CHD2	chr4:1197259-1197736	GM12878	blood:	n/a	n/a
13	RCOR1	chr4:1197393-1197662	GM12878	blood:	n/a	n/a
14	TCF12	chr4:1197423-1197603	GM12878	blood:	n/a	n/a
15	RUNX3	chr4:1197244-1197786	GM12878	blood:	n/a	n/a
16	IRF4	chr4:1197225-1197779	GM12878	blood:	n/a	n/a
17	STAT5A	chr4:1197304-1197729	GM12878	blood:	n/a	n/a
18	EP300	chr4:1197251-1198033	GM12878	blood:	n/a	n/a
19	EP300	chr4:1197333-1197695	GM12878	blood:	n/a	n/a
20	SP1	chr4:1197310-1197714	GM12878	blood:	n/a	n/a
21	MAX	chr4:1197262-1197592	K562	blood:	n/a	n/a
22	ZNF384	chr4:1197313-1197792	GM12878	blood:	n/a	n/a
23	BCL11A	chr4:1197373-1197696	GM12878	blood:	n/a	n/a
24	MAX	chr4:1197445-1197905	NB4	blood:	n/a	n/a
25	ATF2	chr4:1197285-1197761	GM12878	blood:	n/a	n/a
26	STAT3	chr4:1197383-1197750	GM12878	blood:	n/a	n/a
27	WRNIP1	chr4:1197240-1197657	GM12878	blood:	n/a	n/a
28	PAX5	chr4:1197166-1197818	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:1197478-1197602	GM12878	blood:	n/a	n/a
30	MXI1	chr4:1197340-1197689	GM12878	blood:	n/a	n/a
31	POU2F2	chr4:1197302-1197738	GM12891	blood:	n/a	n/a
32	MAX	chr4:1197196-1197839	GM12878	blood:	n/a	n/a
33	PAX5	chr4:1197384-1197634	GM12878	blood:	n/a	n/a
34	USF2	chr4:1197240-1197830	GM12878	blood:	n/a	n/a
35	RUNX3	chr4:1197188-1198012	GM12878	blood:	n/a	n/a
36	EP300	chr4:1197207-1197749	GM12878	blood:	n/a	n/a
37	SMC3	chr4:1197474-1197706	GM12878	blood:	n/a	n/a
38	CUX1	chr4:1197270-1197640	GM12878	blood:	n/a	n/a
39	BHLHE40	chr4:1197268-1197982	GM12878	blood:	n/a	n/a
40	EBF1	chr4:1197327-1197672	GM12878	blood:	n/a	chr4:1197571-1197582
41	POU2F2	chr4:1197310-1197762	GM12878	blood:	n/a	n/a
42	PAX5	chr4:1197346-1197637	GM12878	blood:	n/a	n/a
43	MAZ	chr4:1197291-1197677	GM12878	blood:	n/a	n/a
44	BCLAF1	chr4:1197270-1197692	GM12878	blood:	n/a	n/a
45	BCL11A	chr4:1197300-1197646	GM12878	blood:	n/a	n/a
46	POU2F2	chr4:1197387-1197745	GM12891	blood:	n/a	n/a
47	EBF1	chr4:1197103-1197835	GM12878	blood:	n/a	chr4:1197571-1197582
48	FOXM1	chr4:1197338-1197693	GM12878	blood:	n/a	n/a
49	ATF2	chr4:1197283-1197661	GM12878	blood:	n/a	n/a
50	PBX3	chr4:1197415-1197589	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:1195937..1198894-chr4:1221468..1224458,3	K562	blood:
2	chr4:1196184..1198121-chr4:1199420..1202369,2	K562	blood:
3	chr4:1195791..1198447-chr4:1208482..1210775,2	MCF-7	breast:

No data

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

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1250088	0.89[EUR][1000 genomes]
rs1250106	0.90[ASN][1000 genomes]
rs1250125	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1250126	0.86[EUR][1000 genomes]
rs1265922	0.89[EUR][1000 genomes]
rs56401136	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
rs1250103	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs1250103	RNF212,LOC100132787	cis	cerebellar cortex	BrainEAC
rs1250103	UVSSA	cis	Whole Blood	GTEx
rs1250103	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs1250103	UVSSA	cis	Thyroid	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1185000-1204200	Enhancers	Fetal Muscle Leg	muscle
2	chr4:1193200-1197600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:1193400-1197600	Enhancers	Primary hematopoietic stem cells	blood
4	chr4:1194200-1207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:1194600-1201600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:1194600-1202400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:1194800-1199600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:1194800-1200400	Weak transcription	Ovary	ovary
9	chr4:1194800-1201400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:1194800-1201800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:1194800-1201800	Weak transcription	Osteobl	bone
12	chr4:1194800-1202000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:1194800-1203000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:1194800-1203400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:1195000-1198000	Enhancers	Fetal Stomach	stomach
16	chr4:1195000-1201400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:1195000-1201600	Weak transcription	Right Atrium	heart
18	chr4:1195200-1197600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr4:1195200-1198200	Weak transcription	Stomach Mucosa	stomach
20	chr4:1195200-1198400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:1195200-1200000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:1195200-1200600	Weak transcription	Pancreas	Pancrea
23	chr4:1195200-1201200	Enhancers	Spleen	Spleen
24	chr4:1195200-1201400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:1195200-1201600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:1195200-1201600	Weak transcription	Right Ventricle	heart
27	chr4:1195200-1202600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:1195200-1204400	Weak transcription	HMEC	breast
29	chr4:1195200-1214600	Weak transcription	A549	lung
30	chr4:1195400-1197600	Enhancers	Fetal Thymus	thymus
31	chr4:1195400-1198000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr4:1195400-1198800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:1195400-1199600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:1195800-1198200	Enhancers	Fetal Intestine Large	intestine
35	chr4:1195800-1201000	Weak transcription	Fetal Brain Female	brain
36	chr4:1196000-1199000	Enhancers	Primary B cells from peripheral blood	blood
37	chr4:1196200-1197600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:1196200-1198000	Enhancers	Duodenum Mucosa	Duodenum
39	chr4:1196200-1198000	Genic enhancers	Fetal Intestine Small	intestine
40	chr4:1196200-1198400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr4:1196400-1197600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:1196400-1197600	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr4:1196400-1198000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr4:1196400-1198400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:1196400-1198400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr4:1196400-1198400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:1196400-1198800	Weak transcription	Adipose Nuclei	Adipose
48	chr4:1196400-1199200	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr4:1196400-1200800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr4:1196400-1201600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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