Variant report

Variant	rs10436962
Chromosome Location	chr1:212361622-212361623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212335240..212337640-chr1:212359354..212362015,2	K562	blood:
2	chr1:212360202..212362074-chr1:212367468..212369758,2	K562	blood:
3	chr1:212360558..212362622-chr1:212375645..212378227,2	K562	blood:
4	chr1:212359998..212362512-chr1:212365289..212368132,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1009622	0.81[CHB][hapmap]
rs10436976	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119880	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119884	0.82[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs11119885	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs11119887	0.90[EUR][1000 genomes]
rs12038888	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12041554	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12402397	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs12746096	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389369	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs1472226	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2012917	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs2087946	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs2307128	0.91[EUR][1000 genomes]
rs2358452	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs351386	0.81[CHB][hapmap]
rs4362041	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs4500383	0.80[EUR][1000 genomes]
rs6540731	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs6540732	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs6540733	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs6657900	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs6668866	0.96[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes]
rs6679064	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6679796	0.92[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs7519168	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs7542973	0.89[EUR][1000 genomes]
rs7544225	0.81[CHB][hapmap]
rs903121	0.92[CHB][hapmap];0.85[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10436962	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs10436962	TMEM206	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212358000-212362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:212359400-212363400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:212359600-212362200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr1:212359600-212362600	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:212359600-212363000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:212359600-212363200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:212359600-212363200	Enhancers	Adipose Nuclei	Adipose
8	chr1:212359600-212363200	Enhancers	Spleen	Spleen
9	chr1:212359800-212362800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:212360000-212362800	Weak transcription	Small Intestine	intestine
11	chr1:212360200-212362400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:212360400-212361800	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:212360400-212362000	Enhancers	Fetal Thymus	thymus
14	chr1:212360400-212362400	Enhancers	Primary T cells from cord blood	blood
15	chr1:212360400-212363200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:212360400-212365600	Weak transcription	HepG2	liver
17	chr1:212360600-212361800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:212360600-212362800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:212360600-212363000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr1:212360600-212363000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:212360600-212363400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:212360800-212361800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:212360800-212362000	Enhancers	Fetal Muscle Trunk	muscle
24	chr1:212360800-212362000	Enhancers	GM12878-XiMat	blood
25	chr1:212361000-212361800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:212361000-212362800	Enhancers	Esophagus	oesophagus
27	chr1:212361000-212363000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:212361000-212363000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:212361200-212361800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:212361200-212361800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:212361200-212361800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:212361200-212361800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:212361200-212361800	Enhancers	Left Ventricle	heart
34	chr1:212361200-212361800	Enhancers	Osteobl	bone
35	chr1:212361200-212362000	Enhancers	Fetal Muscle Leg	muscle
36	chr1:212361200-212362000	Enhancers	HUVEC	blood vessel
37	chr1:212361200-212362800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:212361200-212362800	Enhancers	Primary B cells from cord blood	blood
39	chr1:212361200-212362800	Enhancers	Primary T cells fromperipheralblood	blood
40	chr1:212361200-212363000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:212361200-212363000	Enhancers	Placenta	Placenta
42	chr1:212361200-212363000	Enhancers	HMEC	breast
43	chr1:212361200-212363600	Enhancers	Lung	lung
44	chr1:212361400-212361800	Flanking Active TSS	NHEK	skin
45	chr1:212361400-212362200	Enhancers	Stomach Mucosa	stomach
46	chr1:212361400-212363000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:212361400-212363200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:212361600-212361800	Weak transcription	Right Atrium	heart
49	chr1:212361600-212362600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr1:212361600-212363000	Weak transcription	Primary monocytes fromperipheralblood	blood

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