Variant report

Variant	rs900030
Chromosome Location	chr4:1193832-1193833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr4:1193586-1193959	GM12878	blood:	n/a	n/a
2	ELK1	chr4:1193585-1193959	GM12878	blood:	n/a	n/a
3	MAZ	chr4:1193680-1195431	IMR90	lung:	n/a	n/a
4	TBL1XR1	chr4:1193585-1193959	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:1193585-1193959	GM12878	blood:	n/a	n/a
6	MAZ	chr4:1193585-1193959	GM12878	blood:	n/a	n/a
7	RCOR1	chr4:1193306-1195437	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1193384..1195405-chr4:1352251..1354490,2	K562	blood:
2	chr4:1192255..1195518-chr4:1197581..1201308,4	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092535.1-1	chr4:1189571-1193835	NONHSAT094677
2	lnc-AC092535.1-1	chr4:1193715-1193835	NONHSAT094682
3	lnc-AC092535.1-1	chr4:1192837-1193835	NONHSAT094680
4	lnc-AC092535.1-1	chr4:1193401-1193835	NONHSAT094681

No data

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000253399	Chromatin interaction
ENSG00000159674	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1009901	0.85[ASN][1000 genomes]
rs13115903	0.83[ASN][1000 genomes]
rs17164549	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17164680	0.88[JPT][hapmap]
rs2011161	0.83[ASN][1000 genomes]
rs2178443	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2279280	0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3729593	0.85[ASN][1000 genomes]
rs3733340	0.82[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs3755919	0.82[ASN][1000 genomes]
rs3755931	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3755936	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3755937	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3755943	0.85[ASN][1000 genomes]
rs3755950	0.86[ASN][1000 genomes]
rs3775106	0.85[ASN][1000 genomes]
rs3775109	0.87[ASN][1000 genomes]
rs3811733	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3892033	0.85[ASN][1000 genomes]
rs57276390	0.91[ASN][1000 genomes]
rs57560821	0.85[ASN][1000 genomes]
rs57890261	0.92[ASN][1000 genomes]
rs60846075	0.85[ASN][1000 genomes]
rs61010940	0.85[ASN][1000 genomes]
rs6840663	0.87[ASN][1000 genomes]
rs6856873	0.85[ASN][1000 genomes]
rs73069911	0.86[ASN][1000 genomes]
rs73793112	0.90[ASN][1000 genomes]
rs73793144	0.83[ASN][1000 genomes]
rs73793145	0.85[ASN][1000 genomes]
rs73793148	0.85[ASN][1000 genomes]
rs73793154	0.85[ASN][1000 genomes]
rs73793165	0.82[ASN][1000 genomes]
rs877987	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs900030	FGFRL1	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:80 , 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	chr4:1184400-1194000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:1185000-1204200	Enhancers	Fetal Muscle Leg	muscle
4	chr4:1185800-1196200	Weak transcription	Small Intestine	intestine
5	chr4:1187000-1197200	Weak transcription	HepG2	liver
6	chr4:1187200-1194000	Weak transcription	Esophagus	oesophagus
7	chr4:1187200-1194400	Weak transcription	A549	lung
8	chr4:1188000-1194400	Weak transcription	Gastric	stomach
9	chr4:1188200-1194400	Weak transcription	Right Atrium	heart
10	chr4:1188400-1194400	Weak transcription	Left Ventricle	heart
11	chr4:1188600-1194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:1188600-1194200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:1188600-1194400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:1188600-1194400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:1188800-1194200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:1189200-1194000	Weak transcription	Ovary	ovary
17	chr4:1189200-1194400	Weak transcription	Brain Anterior Caudate	brain
18	chr4:1189400-1194800	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:1190400-1194200	Weak transcription	Right Ventricle	heart
20	chr4:1191000-1194000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:1191000-1194400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:1191600-1194000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:1192600-1194000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:1192600-1194000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:1192600-1194600	Weak transcription	Liver	Liver
26	chr4:1193000-1194200	Weak transcription	HSMMtube	muscle
27	chr4:1193200-1197600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:1193400-1194000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:1193400-1194000	Enhancers	Colon Smooth Muscle	Colon
30	chr4:1193400-1194200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr4:1193400-1194200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr4:1193400-1194200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:1193400-1194200	Enhancers	Adipose Nuclei	Adipose
34	chr4:1193400-1194200	Enhancers	Spleen	Spleen
35	chr4:1193400-1194400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:1193400-1194400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr4:1193400-1194600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:1193400-1194800	Bivalent Enhancer	Placenta	Placenta
39	chr4:1193400-1194800	Transcr. at gene 5' and 3'	NHLF	lung
40	chr4:1193400-1195000	Bivalent Enhancer	Fetal Stomach	stomach
41	chr4:1193400-1195400	Flanking Active TSS	GM12878-XiMat	blood
42	chr4:1193400-1197000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr4:1193400-1197200	Enhancers	Fetal Lung	lung
44	chr4:1193400-1197600	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:1193600-1194000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr4:1193600-1194000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr4:1193600-1194000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr4:1193600-1194000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr4:1193600-1194200	Enhancers	Fetal Thymus	thymus
50	chr4:1193600-1194400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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