Variant report

Variant	rs1250105
Chromosome Location	chr4:1203265-1203266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1203216-1203282	HUVEC	blood vessel:	n/a	n/a
2	MAZ	chr4:1203195-1204700	IMR90	lung:	n/a	chr4:1203249-1203260 chr4:1204378-1204388
3	POLR2A	chr4:1202811-1203334	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:1203211-1205143	K562	blood:	n/a	n/a
5	POLR2A	chr4:1202921-1203491	MCF-7	breast:	n/a	n/a
6	POLR2A	chr4:1201720-1203300	U87	brain:	n/a	n/a
7	POLR2A	chr4:1203045-1203443	K562	blood:	n/a	n/a
8	GATA1	chr4:1202908-1203722	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1201438..1204113-chr4:1239051..1243365,5	MCF-7	breast:

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

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1250088	0.94[ASN][1000 genomes]
rs1250089	0.90[EUR][1000 genomes]
rs1250091	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1250092	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	0.96[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1250118	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1250126	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1265922	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs1680056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306475	0.91[EUR][1000 genomes]
rs35376712	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4993865	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6821834	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1250105	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs1250105	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs1250105	UVSSA	cis	Whole Blood	GTEx
rs1250105	SPTBN4	trans	multi-tissue	Pritchard
rs1250105	LOC643624	trans	multi-tissue	Pritchard

Chromatin state (count:118 , 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	chr4:1194800-1203400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:1195200-1204400	Weak transcription	HMEC	breast
5	chr4:1195200-1214600	Weak transcription	A549	lung
6	chr4:1196400-1209800	Weak transcription	Primary B cells from cord blood	blood
7	chr4:1196800-1204200	Enhancers	Placenta	Placenta
8	chr4:1196800-1204400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:1197000-1204400	Enhancers	Fetal Muscle Trunk	muscle
10	chr4:1197600-1204400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:1197600-1204600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:1198000-1211200	Genic enhancers	Fetal Stomach	stomach
13	chr4:1198200-1205200	Enhancers	Stomach Mucosa	stomach
14	chr4:1198400-1204000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:1198400-1204400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:1198400-1204600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:1198400-1207000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:1198600-1204800	Weak transcription	GM12878-XiMat	blood
19	chr4:1199000-1204200	Weak transcription	Dnd41	blood
20	chr4:1199000-1205800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:1199200-1207600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:1200000-1205200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:1200200-1204600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:1200400-1206200	Enhancers	Ovary	ovary
25	chr4:1200400-1206400	Genic enhancers	Brain Germinal Matrix	brain
26	chr4:1200600-1204800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:1200600-1205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:1200800-1204600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:1201000-1205000	Enhancers	Fetal Lung	lung
30	chr4:1201000-1205200	Strong transcription	Fetal Brain Female	brain
31	chr4:1201200-1205200	Genic enhancers	Spleen	Spleen
32	chr4:1201400-1203400	Enhancers	Liver	Liver
33	chr4:1201400-1203600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr4:1201400-1204400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:1201400-1204400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:1201400-1204600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr4:1201400-1204600	Enhancers	Fetal Heart	heart
38	chr4:1201400-1204800	Enhancers	Brain Cingulate Gyrus	brain
39	chr4:1201400-1205000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:1201400-1206000	Enhancers	NHDF-Ad	bronchial
41	chr4:1201600-1204200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:1201600-1204400	Enhancers	Colon Smooth Muscle	Colon
43	chr4:1201600-1204400	Genic enhancers	Fetal Intestine Small	intestine
44	chr4:1201600-1204800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:1201600-1204800	Enhancers	Left Ventricle	heart
46	chr4:1201600-1205000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:1201600-1205000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:1201600-1205000	Enhancers	Right Atrium	heart
49	chr4:1201600-1205200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr4:1201600-1211600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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