Variant report

Variant	rs3920174
Chromosome Location	chr5:118690483-118690484
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	chr5:118688526-118696061	GM12878	blood:	n/a	n/a
2	MEF2A	chr5:118690025-118690687	GM12878	blood:	n/a	n/a
3	EBF1	chr5:118690413-118690528	GM12878	blood:	n/a	n/a
4	TBP	chr5:118689422-118692594	GM12878	blood:	n/a	n/a
5	REST	chr5:118690312-118690549	Hela-S3	cervix:	n/a	n/a
6	PML	chr5:118690397-118693186	GM12878	blood:	n/a	chr5:118692075-118692083
7	POLR2A	chr5:118690288-118692832	GM12892	blood:	n/a	n/a
8	NFATC1	chr5:118689506-118690502	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:118690266-118692633	GM12892	blood:	n/a	n/a
10	NFIC	chr5:118689581-118690843	GM12878	blood:	n/a	n/a
11	CHD1	chr5:118688941-118694425	GM12878	blood:	n/a	n/a
12	FOXM1	chr5:118690381-118691171	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:118690468-118692879	GM18526	blood:	n/a	n/a
14	TBL1XR1	chr5:118689457-118690748	GM12878	blood:	n/a	n/a
15	SPI1	chr5:118690231-118690625	HL-60	blood:	n/a	n/a
16	ATF2	chr5:118689343-118690645	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:118689028-118697007	GM18505	blood:	n/a	n/a
18	POLR2A	chr5:118689433-118694184	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:118688841-118700411	GM12891	blood:	n/a	n/a
20	POLR2A	chr5:118689446-118694162	GM19099	blood:	n/a	n/a
21	POLR2A	chr5:118689533-118692735	GM18951	blood:	n/a	n/a
22	MXI1	chr5:118690298-118690601	GM12878	blood:	n/a	n/a
23	SPI1	chr5:118690260-118690521	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:118690398-118692628	GM12892	blood:	n/a	n/a
25	MTA3	chr5:118688980-118694183	GM12878	blood:	n/a	n/a
26	SPI1	chr5:118690263-118690515	GM12891	blood:	n/a	n/a
27	ATF2	chr5:118689827-118690698	GM12878	blood:	n/a	n/a
28	CEBPB	chr5:118689348-118690599	GM12878	blood:	n/a	chr5:118689562-118689573 chr5:118690262-118690273
29	SPI1	chr5:118690300-118690938	GM12891	blood:	n/a	n/a
30	RCOR1	chr5:118690415-118690837	GM12878	blood:	n/a	n/a
31	SPI1	chr5:118690211-118690561	HL-60	blood:	n/a	n/a
32	NFIC	chr5:118689422-118691329	GM12878	blood:	n/a	n/a
33	CUX1	chr5:118690387-118690558	GM12878	blood:	n/a	n/a
34	SPI1	chr5:118690112-118691013	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:118690428-118692509	GM15510	blood:	n/a	n/a

Variant related genes	Relation type
TNFAIP8	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10059175	0.82[AFR][1000 genomes]
rs10477585	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1112247	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13155880	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1396609	0.83[AFR][1000 genomes]
rs17145265	0.83[AFR][1000 genomes]
rs250298	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs250299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs250308	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32653	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32655	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32657	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs32658	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3797339	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797341	0.86[AFR][1000 genomes]
rs3797343	0.86[AFR][1000 genomes]
rs3813308	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408095	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67328001	0.81[AFR][1000 genomes]
rs6863311	0.84[AFR][1000 genomes]
rs6864305	0.82[AFR][1000 genomes]
rs6869512	0.88[AFR][1000 genomes]
rs6876224	0.86[AFR][1000 genomes]
rs6877025	0.84[AFR][1000 genomes]
rs6882237	0.84[AFR][1000 genomes]
rs6891084	0.85[AFR][1000 genomes]
rs6896277	0.86[AFR][1000 genomes]
rs6896553	0.86[AFR][1000 genomes]
rs6896559	0.86[AFR][1000 genomes]
rs7707470	0.86[AFR][1000 genomes]
rs996934	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882775	chr5:118669094-118691888	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118670800-118691000	Weak transcription	Aorta	Aorta
2	chr5:118671200-118695400	Weak transcription	A549	lung
3	chr5:118676800-118691400	Weak transcription	Lung	lung
4	chr5:118678000-118690600	Weak transcription	NHEK	skin
5	chr5:118679000-118690600	Weak transcription	Fetal Intestine Small	intestine
6	chr5:118679000-118690800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:118680200-118690600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:118680200-118690600	Weak transcription	Colonic Mucosa	Colon
9	chr5:118680400-118690600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr5:118680800-118691000	Weak transcription	HSMMtube	muscle
11	chr5:118682600-118690600	Weak transcription	Thymus	Thymus
12	chr5:118682600-118693600	Weak transcription	Dnd41	blood
13	chr5:118684000-118690600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:118684000-118690800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:118684000-118691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:118684000-118691000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:118684000-118692800	Weak transcription	K562	blood
18	chr5:118684200-118691000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:118685000-118691000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:118685400-118690800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:118687200-118690800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr5:118687800-118691000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:118687800-118691000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr5:118688000-118691000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr5:118688200-118690800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr5:118688600-118691200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:118688800-118690600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:118688800-118690600	Enhancers	Fetal Kidney	kidney
29	chr5:118688800-118691000	Enhancers	Adipose Nuclei	Adipose
30	chr5:118688800-118691400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:118689000-118690600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:118689000-118690800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr5:118689000-118691000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr5:118689000-118691000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:118689000-118691000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:118689000-118691000	Enhancers	Fetal Stomach	stomach
37	chr5:118689000-118691200	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr5:118689000-118691200	Enhancers	Placenta	Placenta
39	chr5:118689000-118691200	Enhancers	NHDF-Ad	bronchial
40	chr5:118689000-118691400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr5:118689200-118690800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:118689200-118691000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr5:118689200-118691200	Enhancers	Fetal Heart	heart
44	chr5:118689400-118691000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:118689400-118691200	Enhancers	Fetal Thymus	thymus
46	chr5:118689400-118691400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:118689600-118690600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:118689600-118690600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:118689600-118690800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
50	chr5:118689600-118691000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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