Variant report

Variant	rs1756011
Chromosome Location	chr4:130019663-130019664
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	RCOR1	chr4:130019662-130020297	K562	blood:	n/a	n/a
2	PML	chr4:130019562-130020121	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:130019234..130021165-chr4:130030871..130032869,2	K562	blood:
2	chr4:130011776..130014103-chr4:130019273..130020805,2	K562	blood:
3	chr4:130017343..130020226-chr4:130031173..130032927,2	K562	blood:

Variant related genes	Relation type
SCLT1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10028974	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11098994	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12500557	0.95[YRI][hapmap]
rs1376202	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs172168	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1757926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757937	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1757938	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757942	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1838911	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs189236	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2118045	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2592948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2597837	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2655311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2777822	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2777823	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs280594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs280596	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280597	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs280601	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3099902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3113487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3113488	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337276	0.84[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs337279	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55865936	0.85[ASN][1000 genomes]
rs62316971	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62316978	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6847784	0.81[YRI][hapmap]
rs7654405	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs796886	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1756011	C4orf33	cis	Artery Tibial	GTEx
rs1756011	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs1756011	LOC132321	cis	normal skin	skin_eQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130017600-130024600	Weak transcription	Fetal Brain Male	brain
2	chr4:130017600-130031400	Weak transcription	Pancreas	Pancrea
3	chr4:130017600-130031400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:130017600-130040400	Weak transcription	Lung	lung
5	chr4:130017800-130024200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:130017800-130026400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:130017800-130027200	Weak transcription	Small Intestine	intestine
8	chr4:130017800-130030800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:130017800-130031400	Weak transcription	Aorta	Aorta
10	chr4:130017800-130031400	Weak transcription	Left Ventricle	heart
11	chr4:130017800-130031400	Weak transcription	Ovary	ovary
12	chr4:130017800-130031400	Weak transcription	Right Ventricle	heart
13	chr4:130017800-130031600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:130017800-130032600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:130017800-130032800	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:130017800-130033400	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:130017800-130033400	Weak transcription	Thymus	Thymus
18	chr4:130017800-130034200	Weak transcription	Colonic Mucosa	Colon
19	chr4:130018000-130019800	Weak transcription	A549	lung
20	chr4:130018000-130021400	Weak transcription	Right Atrium	heart
21	chr4:130018000-130023600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr4:130018000-130023800	Weak transcription	Liver	Liver
23	chr4:130018000-130024400	Weak transcription	Placenta	Placenta
24	chr4:130018000-130024400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:130018000-130024600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:130018000-130024600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:130018000-130024600	Weak transcription	Fetal Lung	lung
28	chr4:130018000-130024800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:130018000-130024800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:130018000-130024800	Weak transcription	Adipose Nuclei	Adipose
31	chr4:130018000-130024800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:130018000-130025400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:130018000-130026400	Weak transcription	Fetal Kidney	kidney
34	chr4:130018000-130028000	Weak transcription	NH-A	brain
35	chr4:130018000-130030200	Weak transcription	Primary T cells from cord blood	blood
36	chr4:130018000-130030400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr4:130018000-130030600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:130018000-130031000	Weak transcription	Fetal Thymus	thymus
39	chr4:130018000-130031400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:130018000-130031400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:130018000-130031400	Weak transcription	Fetal Stomach	stomach
42	chr4:130018000-130032400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:130018000-130033000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:130018000-130033200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:130018000-130033400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:130018000-130034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:130018000-130038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr4:130018200-130024600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:130018200-130024600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:130018200-130024600	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links