Variant report

Variant	rs1569842
Chromosome Location	chr1:184458324-184458325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:183993826..183996650-chr1:184457507..184459731,2	K562	blood:
2	chr1:184453612..184455320-chr1:184457284..184460074,3	MCF-7	breast:
3	chr1:184456316..184459297-chr1:184462033..184464590,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1007224	0.87[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap]
rs10737253	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797971	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10797972	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10911606	0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap]
rs11588922	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12125349	0.80[ASN][1000 genomes]
rs12127674	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1339563	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1339564	0.83[ASN][1000 genomes]
rs1339565	0.80[ASN][1000 genomes]
rs1339566	0.87[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs1416751	0.88[CEU][hapmap]
rs1884200	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2001270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2038307	0.89[ASN][1000 genomes]
rs2038308	0.87[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap]
rs2180073	0.87[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs2180077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207528	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378888	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2890015	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4650667	0.83[ASN][1000 genomes]
rs4651208	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4651210	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4651211	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4651216	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4651217	0.80[ASN][1000 genomes]
rs55729410	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661707	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6666704	0.99[ASN][1000 genomes]
rs7517518	0.96[ASN][1000 genomes]
rs7533466	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7544240	0.80[ASN][1000 genomes]
rs9633308	0.88[CEU][hapmap]
rs9970984	0.83[ASN][1000 genomes]
rs9970990	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1569842	TDRD5	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184444600-184460400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:184449200-184460600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr1:184449800-184459800	Enhancers	Psoas Muscle	Psoas
4	chr1:184450200-184463200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:184451400-184463600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:184451600-184459200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:184452600-184458800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:184452600-184459600	Weak transcription	NH-A	brain
9	chr1:184452800-184459200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:184454000-184461400	Weak transcription	Gastric	stomach
11	chr1:184454200-184461800	Weak transcription	Fetal Brain Male	brain
12	chr1:184454400-184459200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:184454400-184459400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:184454800-184459600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr1:184455200-184482000	Weak transcription	Esophagus	oesophagus
16	chr1:184455400-184458400	Weak transcription	HSMM	muscle
17	chr1:184455400-184460400	Weak transcription	Placenta	Placenta
18	chr1:184455600-184459200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:184455600-184459200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:184455600-184459200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:184455600-184459200	Weak transcription	A549	lung
22	chr1:184455600-184459400	Weak transcription	HMEC	breast
23	chr1:184455800-184459200	Weak transcription	Osteobl	bone
24	chr1:184455800-184460400	Weak transcription	HSMMtube	muscle
25	chr1:184455800-184466200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:184456200-184459000	Weak transcription	NHDF-Ad	bronchial
27	chr1:184456200-184459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:184456200-184459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:184456200-184459200	Weak transcription	Pancreas	Pancrea
30	chr1:184456200-184460400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:184456200-184462800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:184456200-184464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:184456400-184459200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:184456400-184459200	Weak transcription	NHEK	skin
35	chr1:184456400-184460400	Weak transcription	Colonic Mucosa	Colon
36	chr1:184456400-184460400	Weak transcription	Spleen	Spleen
37	chr1:184456400-184460600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:184456400-184460800	Weak transcription	Fetal Lung	lung
39	chr1:184456400-184460800	Weak transcription	Lung	lung
40	chr1:184456400-184461400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:184456400-184465200	Weak transcription	Fetal Brain Female	brain
42	chr1:184456400-184502200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:184456600-184459000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:184456600-184459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:184456600-184459200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:184456600-184459200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:184456600-184459200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:184456600-184460200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:184456600-184460200	Weak transcription	GM12878-XiMat	blood
50	chr1:184456600-184460200	Weak transcription	Monocytes-CD14+_RO01746	blood

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