Variant report

Variant	rs1991223
Chromosome Location	chr4:153019169-153019170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13140099	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13151283	0.82[EUR][1000 genomes]
rs17276450	0.82[EUR][1000 genomes]
rs17361216	0.80[EUR][1000 genomes]
rs34067446	0.80[EUR][1000 genomes]
rs34509512	0.82[EUR][1000 genomes]
rs35336515	0.82[EUR][1000 genomes]
rs35897176	0.82[EUR][1000 genomes]
rs747110	0.85[CHB][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1991223	LXN	trans	lymphoblastoid	seeQTL
rs1991223	RP11-18H21.1	cis	Whole Blood	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:153009600-153021600	Enhancers	Thymus	Thymus
2	chr4:153010200-153020200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr4:153010200-153021000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr4:153010200-153021200	Enhancers	Primary T cells from cord blood	blood
5	chr4:153010400-153020000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr4:153013800-153021200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr4:153014000-153023400	Weak transcription	Fetal Brain Female	brain
8	chr4:153014200-153021600	Enhancers	Fetal Thymus	thymus
9	chr4:153014600-153021200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr4:153015200-153021600	Enhancers	Dnd41	blood
11	chr4:153015400-153020000	Weak transcription	Spleen	Spleen
12	chr4:153015400-153020600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr4:153015400-153021000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:153015600-153020600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:153015600-153021600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:153016000-153020200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:153016400-153023600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:153016600-153021600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:153016600-153022000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:153016800-153019800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:153016800-153022800	Weak transcription	Fetal Heart	heart
22	chr4:153017000-153021600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:153017000-153021600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:153017200-153021200	Weak transcription	NHEK	skin
25	chr4:153017200-153021600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:153017200-153021600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:153017200-153021800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:153017200-153022600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:153017200-153027000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:153017400-153021600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr4:153017400-153022000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:153018000-153022000	Weak transcription	Stomach Mucosa	stomach
33	chr4:153018000-153023400	Weak transcription	HSMMtube	muscle
34	chr4:153018200-153020000	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:153018200-153021200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr4:153018200-153021800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:153018600-153022000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:153018800-153019400	Enhancers	Primary B cells from cord blood	blood
39	chr4:153019000-153019400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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