Variant report

Variant	rs1553444
Chromosome Location	chr1:161813515-161813516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10733044	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10737502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753645	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753666	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800068	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1394070	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134690	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2134696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341468	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2341479	0.94[ASN][1000 genomes]
rs2499855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2499856	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2880055	0.94[ASN][1000 genomes]
rs34312480	0.94[ASN][1000 genomes]
rs34461550	0.97[ASN][1000 genomes]
rs35621393	1.00[ASN][1000 genomes]
rs36080602	0.94[ASN][1000 genomes]
rs3767633	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233380	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4300199	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4579731	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656335	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656339	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4657103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427633	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427639	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6667896	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685369	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698065	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6701754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs71639910	0.92[ASN][1000 genomes]
rs7517386	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532448	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs924777	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
7	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1553444	NTRK1	cis	parietal	SCAN
rs1553444	FCGR2B	cis	multi-tissue	Pritchard
rs1553444	PEA15	cis	parietal	SCAN
rs1553444	FCRLM2	cis	multi-tissue	Pritchard
rs1553444	TAGLN2	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161773400-161854400	Weak transcription	Small Intestine	intestine
2	chr1:161780400-161824400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:161780600-161823400	Weak transcription	A549	lung
4	chr1:161780600-161836600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:161780800-161823000	Weak transcription	HSMMtube	muscle
6	chr1:161780800-161825800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:161780800-161834000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:161781000-161823000	Weak transcription	Fetal Kidney	kidney
9	chr1:161785400-161822400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:161787600-161821000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:161790200-161816000	Weak transcription	NHEK	skin
12	chr1:161791400-161823000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:161791600-161816200	Weak transcription	HepG2	liver
14	chr1:161791600-161823000	Weak transcription	Fetal Lung	lung
15	chr1:161791800-161819800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:161791800-161820800	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:161791800-161822400	Weak transcription	Thymus	Thymus
18	chr1:161791800-161823000	Weak transcription	Fetal Brain Female	brain
19	chr1:161791800-161823600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:161791800-161842000	Weak transcription	Brain Angular Gyrus	brain
21	chr1:161792000-161822400	Weak transcription	Aorta	Aorta
22	chr1:161792000-161823200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:161792200-161816000	Weak transcription	Brain Anterior Caudate	brain
24	chr1:161792200-161816200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:161792200-161816800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:161792200-161821000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:161792200-161838000	Weak transcription	Fetal Brain Male	brain
28	chr1:161792600-161818600	Weak transcription	Ovary	ovary
29	chr1:161792800-161816000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:161795200-161860200	Weak transcription	Lung	lung
31	chr1:161795400-161822400	Weak transcription	Fetal Stomach	stomach
32	chr1:161795600-161823000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:161795800-161827600	Weak transcription	Gastric	stomach
34	chr1:161795800-161859000	Weak transcription	Pancreas	Pancrea
35	chr1:161796000-161820600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:161797800-161818600	Weak transcription	NHLF	lung
37	chr1:161798200-161819800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:161798600-161816000	Weak transcription	K562	blood
39	chr1:161798600-161820000	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:161798800-161818200	Weak transcription	Fetal Heart	heart
41	chr1:161802200-161823200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:161802400-161825000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:161805800-161814800	Strong transcription	Primary T cells from cord blood	blood
44	chr1:161805800-161838200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:161805800-161846200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:161806200-161816000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:161806200-161825600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:161806400-161822600	Weak transcription	Brain Germinal Matrix	brain
49	chr1:161807000-161814800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:161807000-161822400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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