Variant report

Variant	rs2134697
Chromosome Location	chr1:161780979-161780980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10436881	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs10494357	0.90[AFR][1000 genomes]
rs10800032	0.92[AFR][1000 genomes]
rs10800079	0.81[AFR][1000 genomes]
rs10917876	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs10917968	0.92[AFR][1000 genomes]
rs10918341	0.95[CHB][hapmap];0.92[JPT][hapmap]
rs10918342	1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs12024729	0.85[YRI][hapmap]
rs12045320	0.86[AFR][1000 genomes]
rs12045333	0.89[YRI][hapmap]
rs12081397	0.87[AFR][1000 genomes]
rs12086247	1.00[ASW][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs12124369	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12405111	0.85[YRI][hapmap]
rs1354370	0.85[YRI][hapmap]
rs1394066	0.86[AFR][1000 genomes]
rs1503807	0.85[YRI][hapmap]
rs1503815	0.86[AFR][1000 genomes]
rs16860777	0.85[YRI][hapmap]
rs1875762	0.91[AFR][1000 genomes]
rs2089083	0.85[YRI][hapmap]
rs2271010	0.85[YRI][hapmap]
rs2340715	0.85[YRI][hapmap]
rs2341475	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2880056	0.85[YRI][hapmap]
rs3767636	0.87[AFR][1000 genomes]
rs3767637	0.87[AFR][1000 genomes]
rs6427632	0.85[AFR][1000 genomes]
rs7513303	0.85[YRI][hapmap]
rs7516955	0.81[AFR][1000 genomes]
rs7518743	0.93[AFR][1000 genomes]
rs7550803	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2134697	NTRK1	cis	parietal	SCAN
rs2134697	F11R	cis	parietal	SCAN
rs2134697	C1orf61	cis	parietal	SCAN
rs2134697	DUSP12	cis	lymphoblastoid	seeQTL
rs2134697	FCRLA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161738600-161794000	Weak transcription	Pancreas	Pancrea
2	chr1:161738600-161795600	Weak transcription	Gastric	stomach
3	chr1:161753400-161800600	Weak transcription	Spleen	Spleen
4	chr1:161755000-161793600	Weak transcription	Colonic Mucosa	Colon
5	chr1:161757400-161797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:161762200-161790600	Weak transcription	Fetal Brain Male	brain
7	chr1:161762400-161790800	Weak transcription	NH-A	brain
8	chr1:161762400-161791200	Weak transcription	Right Ventricle	heart
9	chr1:161762400-161795400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:161762800-161797600	Weak transcription	HMEC	breast
11	chr1:161763000-161797400	Weak transcription	NHLF	lung
12	chr1:161766000-161790800	Weak transcription	Lung	lung
13	chr1:161767400-161791200	Weak transcription	Aorta	Aorta
14	chr1:161768000-161789400	Weak transcription	HepG2	liver
15	chr1:161772000-161782200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:161772200-161789400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:161772600-161785800	Weak transcription	Hela-S3	cervix
18	chr1:161773000-161790600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:161773400-161789800	Weak transcription	Brain Substantia Nigra	brain
20	chr1:161773400-161790800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:161773400-161797200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:161773400-161854400	Weak transcription	Small Intestine	intestine
23	chr1:161774600-161786000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:161775800-161794800	Weak transcription	Fetal Stomach	stomach
25	chr1:161776400-161787000	Weak transcription	Fetal Heart	heart
26	chr1:161776600-161785800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:161776800-161785800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:161776800-161789400	Weak transcription	Placenta	Placenta
29	chr1:161777600-161786000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:161778600-161782400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:161779400-161781200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:161779600-161781200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:161779800-161781000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:161779800-161781000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:161779800-161781000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:161779800-161781000	Strong transcription	Adipose Nuclei	Adipose
37	chr1:161779800-161781000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:161779800-161781000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:161779800-161781000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:161779800-161781000	Strong transcription	K562	blood
41	chr1:161779800-161781200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:161779800-161781400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
43	chr1:161779800-161781600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:161779800-161781800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:161779800-161782600	Strong transcription	Fetal Thymus	thymus
46	chr1:161779800-161783200	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:161780000-161781000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:161780000-161781000	ZNF genes & repeats	Fetal Kidney	kidney
49	chr1:161780000-161781200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:161780000-161781600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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