Variant report

Variant	rs1250127
Chromosome Location	chr4:1189630-1189631
allele	C/T
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	chr4:1189397-1189935	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1189059..1190794-chr4:1239654..1242349,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092535.1-1	chr4:1189571-1193835	NONHSAT094677
2	lnc-AC092535.1-1	chr4:1189572-1191603	NONHSAT094678

Variant related genes	Relation type
SPON2	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11932230	1.00[EUR][1000 genomes]
rs1250087	1.00[EUR][1000 genomes]
rs1272043	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1680077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2127909	1.00[EUR][1000 genomes]
rs4246689	1.00[EUR][1000 genomes]
rs4974626	1.00[EUR][1000 genomes]
rs4974635	1.00[EUR][1000 genomes]
rs4974645	1.00[EUR][1000 genomes]
rs57106389	1.00[EUR][1000 genomes]
rs58168130	1.00[EUR][1000 genomes]
rs61053739	1.00[EUR][1000 genomes]
rs6836809	1.00[EUR][1000 genomes]
rs6836952	1.00[EUR][1000 genomes]
rs7659524	1.00[EUR][1000 genomes]
rs7676912	1.00[EUR][1000 genomes]
rs900031	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	esv3394271	chr4:1187577-1190125	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1180800-1194000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:1181200-1193400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr4:1181200-1193600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr4:1181600-1190000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:1181600-1190000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:1181600-1193600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:1182600-1190200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:1184400-1194000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:1185000-1204200	Enhancers	Fetal Muscle Leg	muscle
10	chr4:1185200-1190000	Enhancers	Fetal Stomach	stomach
11	chr4:1185200-1190400	Bivalent Enhancer	Placenta	Placenta
12	chr4:1185400-1190400	Enhancers	Right Ventricle	heart
13	chr4:1185800-1196200	Weak transcription	Small Intestine	intestine
14	chr4:1187000-1197200	Weak transcription	HepG2	liver
15	chr4:1187200-1194000	Weak transcription	Esophagus	oesophagus
16	chr4:1187200-1194400	Weak transcription	A549	lung
17	chr4:1188000-1190600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:1188000-1193800	Weak transcription	Stomach Mucosa	stomach
19	chr4:1188000-1194400	Weak transcription	Gastric	stomach
20	chr4:1188200-1193600	Weak transcription	Fetal Thymus	thymus
21	chr4:1188200-1194400	Weak transcription	Right Atrium	heart
22	chr4:1188400-1190000	Weak transcription	Liver	Liver
23	chr4:1188400-1190200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:1188400-1190400	Weak transcription	Lung	lung
25	chr4:1188400-1193800	Weak transcription	Fetal Intestine Large	intestine
26	chr4:1188400-1194400	Weak transcription	Left Ventricle	heart
27	chr4:1188600-1189800	Enhancers	Adipose Nuclei	Adipose
28	chr4:1188600-1189800	Enhancers	Stomach Smooth Muscle	stomach
29	chr4:1188600-1189800	Weak transcription	Thymus	Thymus
30	chr4:1188600-1190200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:1188600-1190400	Weak transcription	NHDF-Ad	bronchial
32	chr4:1188600-1190600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:1188600-1190600	Enhancers	Fetal Muscle Trunk	muscle
34	chr4:1188600-1191000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:1188600-1192000	Weak transcription	HSMMtube	muscle
36	chr4:1188600-1192000	Weak transcription	NH-A	brain
37	chr4:1188600-1193400	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:1188600-1193800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:1188600-1194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:1188600-1194200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:1188600-1194400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:1188600-1194400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:1188800-1193600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:1188800-1194200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:1189200-1190000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:1189200-1190400	Genic enhancers	Spleen	Spleen
47	chr4:1189200-1190800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:1189200-1191400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:1189200-1192000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:1189200-1192000	Weak transcription	HSMM	muscle

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