Variant report

Variant	rs3783637
Chromosome Location	chr14:55348118-55348119
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	RFX5	chr14:55348044-55349924	SK-N-SH	brain:	n/a	chr14:55349620-55349629 chr14:55349597-55349605
2	TAF1	chr14:55347970-55348442	GM12878	blood:	n/a	n/a
3	BATF	chr14:55347981-55348418	GM12878	blood:	n/a	n/a
4	POLR2A	chr14:55348066-55348528	GM12892	blood:	n/a	n/a
5	PML	chr14:55347841-55348972	GM12878	blood:	n/a	n/a
6	FOXM1	chr14:55347932-55348410	GM12878	blood:	n/a	n/a
7	IRF1	chr14:55348040-55348260	K562	blood:	n/a	chr14:55348193-55348206 chr14:55348190-55348204 chr14:55348194-55348208 chr14:55348193-55348206 chr14:55348188-55348205 chr14:55348193-55348206 chr14:55348172-55348188 chr14:55348194-55348204 chr14:55348192-55348203 chr14:55348193-55348207 chr14:55348193-55348204
8	POLR2A	chr14:55348059-55348357	GM12892	blood:	n/a	n/a
9	POLR2A	chr14:55348056-55348862	HUVEC	blood vessel:	n/a	n/a
10	WRNIP1	chr14:55348003-55348489	GM12878	blood:	n/a	n/a
11	BCLAF1	chr14:55347924-55348724	GM12878	blood:	n/a	chr14:55348195-55348204
12	BATF	chr14:55347926-55348447	GM12878	blood:	n/a	n/a
13	TBP	chr14:55347985-55349003	GM12878	blood:	n/a	n/a
14	MTA3	chr14:55347981-55348942	GM12878	blood:	n/a	n/a
15	MTA3	chr14:55347857-55348866	GM12878	blood:	n/a	n/a
16	CTCF	chr14:55348040-55348190	GM06990	blood:	n/a	n/a
17	ATF2	chr14:55348036-55348807	GM12878	blood:	n/a	n/a
18	POLR2A	chr14:55347929-55349095	GM12878	blood:	n/a	n/a
19	RUNX3	chr14:55348008-55348483	GM12878	blood:	n/a	n/a
20	JUND	chr14:55347787-55348426	GM12878	blood:	n/a	chr14:55348201-55348213
21	EBF1	chr14:55348030-55348781	GM12878	blood:	n/a	n/a
22	BCLAF1	chr14:55347970-55348963	GM12878	blood:	n/a	chr14:55348195-55348204 chr14:55348801-55348810
23	POLR2A	chr14:55347917-55348408	GM12878	blood:	n/a	n/a
24	NFIC	chr14:55347944-55348464	GM12878	blood:	n/a	n/a
25	EP300	chr14:55347996-55348597	GM12878	blood:	n/a	chr14:55348166-55348180
26	MXI1	chr14:55347981-55348944	GM12878	blood:	n/a	n/a
27	YY1	chr14:55348075-55348712	GM12878	blood:	n/a	chr14:55348322-55348332
28	ZNF384	chr14:55347932-55348385	GM12878	blood:	n/a	n/a
29	EBF1	chr14:55347926-55348182	GM12878	blood:	n/a	n/a
30	EP300	chr14:55347820-55350131	SK-N-SH	brain:	n/a	chr14:55348166-55348180 chr14:55348796-55348810 chr14:55348744-55348752
31	IRF1	chr14:55348012-55349360	K562	blood:	n/a	chr14:55348193-55348206 chr14:55348801-55348815 chr14:55348190-55348204 chr14:55348801-55348811 chr14:55348194-55348208 chr14:55348193-55348206 chr14:55348797-55348811 chr14:55348188-55348205 chr14:55348193-55348206 chr14:55349323-55349339 chr14:55348172-55348188 chr14:55348194-55348204 chr14:55348801-55348812 chr14:55348799-55348812 chr14:55348192-55348203 chr14:55348802-55348813 chr14:55348193-55348207 chr14:55348799-55348812 chr14:55348799-55348812 chr14:55348464-55348478 chr14:55348193-55348204
32	CTCF	chr14:55347911-55348456	GM12878	blood:	n/a	n/a
33	MYC	chr14:55348070-55348256	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr14:55348002-55348835	GM12892	blood:	n/a	n/a
35	ATF2	chr14:55347965-55348455	GM12878	blood:	n/a	n/a
36	CTCF	chr14:55348078-55348384	Spleen_OC	spleen:	n/a	n/a
37	FOXM1	chr14:55347808-55348331	GM12878	blood:	n/a	n/a
38	MXI1	chr14:55347817-55349899	SK-N-SH	brain:	n/a	n/a
39	ZNF143	chr14:55347988-55348916	GM12878	blood:	n/a	n/a
40	IKZF1	chr14:55347994-55348296	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
MIR4308	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10139282	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873086	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158027	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12147422	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17128050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2183080	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs28477407	0.80[ASN][1000 genomes]
rs28757745	0.80[ASN][1000 genomes]
rs3783638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825611	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61702394	0.80[ASN][1000 genomes]
rs66989494	0.83[EUR][1000 genomes]
rs7492600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8003903	0.92[EUR][1000 genomes]
rs8004018	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8004445	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010282	1.00[CEU][hapmap]
rs8010461	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3323442	chr14:55346027-55348775	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	esv3358447	chr14:55346377-55348700	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	esv3322576	chr14:55346802-55348400	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

Variant related diseases (count:2)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog
Rheumatoid arthritis	22446963	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3783637	GCH1	cis	parietal	SCAN
rs3783637	L2HGDH	cis	parietal	SCAN
rs3783637	GCH1	cis	cerebellum	SCAN
rs3783637	WDHD1	cis	cerebellum	SCAN
rs3783637	GCH1	Cis_1M	lymphoblastoid	RTeQTL
rs3783637	KTN1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55337600-55348600	Weak transcription	Hela-S3	cervix
2	chr14:55343800-55348200	Weak transcription	Fetal Intestine Large	intestine
3	chr14:55345400-55348200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:55345400-55354800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr14:55345400-55368200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:55347600-55348200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr14:55347600-55348200	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr14:55347600-55348400	Flanking Active TSS	Liver	Liver
9	chr14:55347600-55349000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr14:55347600-55349200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr14:55347600-55349400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr14:55347600-55349400	Flanking Active TSS	Dnd41	blood
13	chr14:55347800-55348200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr14:55347800-55348200	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr14:55347800-55348200	Active TSS	Fetal Muscle Leg	muscle
16	chr14:55347800-55348200	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr14:55347800-55348400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr14:55347800-55348400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr14:55347800-55348400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr14:55347800-55348400	Active TSS	GM12878-XiMat	blood
21	chr14:55347800-55348600	Active TSS	Muscle Satellite Cultured Cells	--
22	chr14:55347800-55348600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr14:55347800-55348600	Active TSS	Monocytes-CD14+_RO01746	blood
24	chr14:55347800-55348800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:55347800-55348800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr14:55347800-55348800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr14:55347800-55348800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr14:55347800-55348800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr14:55347800-55348800	Active TSS	Right Atrium	heart
30	chr14:55347800-55348800	Active TSS	NHDF-Ad	bronchial
31	chr14:55347800-55348800	Active TSS	NHLF	lung
32	chr14:55347800-55349000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr14:55347800-55349000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr14:55347800-55349000	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr14:55347800-55349000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr14:55347800-55349000	Active TSS	Aorta	Aorta
37	chr14:55347800-55349000	Active TSS	Psoas Muscle	Psoas
38	chr14:55347800-55349000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr14:55347800-55349000	Active TSS	Thymus	Thymus
40	chr14:55347800-55349000	Flanking Active TSS	HMEC	breast
41	chr14:55347800-55349200	Active TSS	Rectal Smooth Muscle	rectum
42	chr14:55347800-55349200	Flanking Active TSS	NHEK	skin
43	chr14:55347800-55349600	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr14:55348000-55348200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr14:55348000-55348200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr14:55348000-55348200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:55348000-55348200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr14:55348000-55348400	Active TSS	Primary hematopoietic stem cells	blood
49	chr14:55348000-55348400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
50	chr14:55348000-55348400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links