Variant report

Variant	rs338566
Chromosome Location	chr1:184777467-184777468
allele	A/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	POLR2A	chr1:184776805-184777978	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184771660..184773862-chr1:184776214..184778958,2	K562	blood:

Variant related genes	Relation type
FAM129A	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10797988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10797989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10797990	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1857954	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs338561	0.81[ASN][1000 genomes]
rs338562	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs338563	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs338564	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs338565	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs338567	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs338568	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs338570	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs338571	0.84[ASN][1000 genomes]
rs4011648	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4011650	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651234	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs520605	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs521366	0.89[EUR][1000 genomes]
rs533853	0.87[EUR][1000 genomes]
rs543912	0.81[GIH][hapmap]
rs641337	0.81[GIH][hapmap]
rs6424964	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671637	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519082	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906285	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer 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	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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 target site	69 gene(s)	inside rSNPs	diseases
3	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS 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	13 gene(s)	inside rSNPs	diseases
4	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs338566	PRG4	cis	parietal	SCAN
rs338566	EDEM3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184756800-184794000	Weak transcription	Thymus	Thymus
2	chr1:184762000-184781600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:184762000-184787800	Weak transcription	Spleen	Spleen
4	chr1:184762400-184789400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:184762600-184792800	Weak transcription	Colonic Mucosa	Colon
6	chr1:184763000-184782800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:184763800-184781200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:184764800-184779000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:184768000-184809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:184770800-184787000	Weak transcription	Gastric	stomach
11	chr1:184771800-184782800	Weak transcription	NHLF	lung
12	chr1:184772000-184792000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:184772400-184801800	Weak transcription	Primary T cells from cord blood	blood
14	chr1:184772600-184782600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:184772800-184782600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:184772800-184790600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:184773000-184781800	Weak transcription	NHEK	skin
18	chr1:184773200-184809400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:184773600-184780600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:184775200-184781200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:184775200-184781600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:184775200-184787400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:184775400-184777600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:184775400-184780000	Weak transcription	Adipose Nuclei	Adipose
25	chr1:184775400-184780000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:184775400-184783000	Weak transcription	NHDF-Ad	bronchial
27	chr1:184775400-184787800	Weak transcription	Esophagus	oesophagus
28	chr1:184775400-184791600	Weak transcription	Stomach Mucosa	stomach
29	chr1:184775600-184778000	Strong transcription	Fetal Muscle Leg	muscle
30	chr1:184775600-184779800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:184775600-184779800	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:184775600-184781000	Weak transcription	Psoas Muscle	Psoas
33	chr1:184775600-184781800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:184775600-184796800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:184775800-184778000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:184775800-184779000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:184775800-184779600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:184775800-184784200	Weak transcription	Fetal Heart	heart
39	chr1:184775800-184794000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:184776000-184779200	Weak transcription	GM12878-XiMat	blood
41	chr1:184776000-184779800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:184776400-184777800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:184776400-184778000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:184776400-184781800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:184776600-184777800	Strong transcription	Fetal Stomach	stomach
46	chr1:184776600-184778000	Strong transcription	Aorta	Aorta
47	chr1:184776600-184778000	Strong transcription	Right Ventricle	heart
48	chr1:184776600-184782800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:184776800-184777600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr1:184776800-184777600	Strong transcription	Lung	lung

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