Variant report

Variant	rs6685369
Chromosome Location	chr1:161754834-161754835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161745976..161748156-chr1:161753878..161755415,2	K562	blood:
2	chr1:161748440..161753794-chr1:161754106..161757609,6	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10733044	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10737502	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753645	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753666	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10800068	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1394070	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553444	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1806594	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2055539	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2134690	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298019	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341468	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2341479	0.90[ASN][1000 genomes]
rs2499855	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499856	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2880055	0.90[ASN][1000 genomes]
rs34312480	0.90[ASN][1000 genomes]
rs34461550	1.00[ASN][1000 genomes]
rs35621393	0.97[ASN][1000 genomes]
rs36080602	0.90[ASN][1000 genomes]
rs3767633	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233380	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4300199	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4579731	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656335	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656339	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4657103	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427633	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6427639	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6667896	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698065	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6701754	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71639910	0.89[ASN][1000 genomes]
rs7517386	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532448	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs924777	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6685369	TAGLN2	cis	cerebellum	SCAN
rs6685369	NTRK1	cis	parietal	SCAN
rs6685369	PEA15	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161736800-161757200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:161737000-161765600	Weak transcription	Aorta	Aorta
3	chr1:161737200-161761600	Weak transcription	Fetal Brain Male	brain
4	chr1:161737200-161761600	Weak transcription	Right Ventricle	heart
5	chr1:161737200-161775200	Weak transcription	Fetal Stomach	stomach
6	chr1:161737200-161775800	Weak transcription	Stomach Mucosa	stomach
7	chr1:161737200-161780000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:161737600-161762000	Weak transcription	Fetal Lung	lung
9	chr1:161737600-161764600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:161738200-161760200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:161738600-161794000	Weak transcription	Pancreas	Pancrea
12	chr1:161738600-161795600	Weak transcription	Gastric	stomach
13	chr1:161740400-161761800	Weak transcription	Ovary	ovary
14	chr1:161742400-161773000	Weak transcription	Small Intestine	intestine
15	chr1:161745400-161780000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:161747200-161761600	Weak transcription	Thymus	Thymus
17	chr1:161747200-161763000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:161747600-161773800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:161748000-161778800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:161748200-161758400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:161748200-161780000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:161748800-161758400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:161749000-161761600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:161749000-161777000	Strong transcription	Liver	Liver
25	chr1:161749200-161780000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:161749400-161760800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:161750000-161762000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:161750000-161768200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:161750400-161755600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:161750400-161757400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:161750400-161757800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:161750400-161758800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:161750600-161758400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:161750600-161774800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:161750800-161757200	Weak transcription	Brain Germinal Matrix	brain
36	chr1:161750800-161760000	Strong transcription	Hela-S3	cervix
37	chr1:161751200-161758000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:161751200-161758000	Strong transcription	Placenta	Placenta
39	chr1:161751200-161758200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:161751200-161758800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:161751400-161755400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:161751400-161757600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:161751400-161758000	Strong transcription	HUVEC	blood vessel
44	chr1:161751600-161755400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:161751600-161758000	Strong transcription	Primary T cells from cord blood	blood
46	chr1:161751800-161755000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:161751800-161755400	Strong transcription	Primary B cells from cord blood	blood
48	chr1:161751800-161756200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:161751800-161773800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:161752000-161755000	Strong transcription	Brain Anterior Caudate	brain

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