Variant report

Variant	rs10436976
Chromosome Location	chr1:212360408-212360409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212358356..212360548-chr1:212371343..212374301,2	K562	blood:
2	chr1:212335240..212337640-chr1:212359354..212362015,2	K562	blood:
3	chr1:212360202..212362074-chr1:212367468..212369758,2	K562	blood:
4	chr1:212359998..212362512-chr1:212365289..212368132,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1009622	0.81[CHB][hapmap]
rs10436962	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119880	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11119884	0.86[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs11119885	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs11119887	0.90[EUR][1000 genomes]
rs12038888	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12041554	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12402397	0.83[CHB][hapmap]
rs12746096	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389369	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1472226	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap]
rs2012917	0.83[CHB][hapmap]
rs2087946	0.83[CHB][hapmap]
rs2307128	0.91[EUR][1000 genomes]
rs2358452	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs351386	0.81[CHB][hapmap]
rs4362041	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4500383	0.80[EUR][1000 genomes]
rs6540731	0.91[CHB][hapmap];0.97[GIH][hapmap];0.80[EUR][1000 genomes]
rs6540732	0.83[CHB][hapmap];0.97[GIH][hapmap]
rs6540733	0.83[CHB][hapmap]
rs6657900	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs6668866	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs6679064	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6679796	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes]
rs7519168	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs7542973	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7544225	0.81[CHB][hapmap]
rs903121	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10436976	TMEM206	cis	cerebellum	SCAN
rs10436976	LGTN	cis	cerebellum	SCAN
rs10436976	SYT14	cis	cerebellum	SCAN
rs10436976	TMEM206	cis	Esophagus Mucosa	GTEx
rs10436976	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212353000-212361200	Weak transcription	Right Atrium	heart
2	chr1:212353200-212361200	Weak transcription	Lung	lung
3	chr1:212354200-212361200	Weak transcription	HMEC	breast
4	chr1:212355200-212361200	Weak transcription	Left Ventricle	heart
5	chr1:212356000-212360600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:212356200-212361000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:212357800-212361200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:212358000-212361200	Weak transcription	Placenta	Placenta
9	chr1:212358000-212362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:212359400-212363400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:212359600-212360600	Enhancers	Stomach Mucosa	stomach
12	chr1:212359600-212361600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:212359600-212362200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:212359600-212362600	Enhancers	Primary B cells from peripheral blood	blood
15	chr1:212359600-212363000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:212359600-212363200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:212359600-212363200	Enhancers	Adipose Nuclei	Adipose
18	chr1:212359600-212363200	Enhancers	Spleen	Spleen
19	chr1:212359800-212360600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:212359800-212360600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:212359800-212360600	Flanking Active TSS	Dnd41	blood
22	chr1:212359800-212360800	Flanking Active TSS	GM12878-XiMat	blood
23	chr1:212359800-212362800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:212360000-212360600	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:212360000-212360600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:212360000-212360600	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:212360000-212360600	Enhancers	NHEK	skin
28	chr1:212360000-212360800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:212360000-212360800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr1:212360000-212362800	Weak transcription	Small Intestine	intestine
31	chr1:212360200-212360600	Active TSS	Primary T cells fromperipheralblood	blood
32	chr1:212360200-212360600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr1:212360200-212360600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:212360200-212360600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:212360200-212360600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:212360200-212361000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:212360200-212362400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:212360400-212360600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr1:212360400-212360600	Active TSS	Duodenum Mucosa	Duodenum
40	chr1:212360400-212360600	Enhancers	Esophagus	oesophagus
41	chr1:212360400-212360800	Enhancers	Primary B cells from cord blood	blood
42	chr1:212360400-212361000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:212360400-212361800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr1:212360400-212362000	Enhancers	Fetal Thymus	thymus
45	chr1:212360400-212362400	Enhancers	Primary T cells from cord blood	blood
46	chr1:212360400-212363200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:212360400-212365600	Weak transcription	HepG2	liver

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