Variant report

Variant	rs11487952
Chromosome Location	chr1:75195812-75195813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11162945	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1122338	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1133891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11485264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11485299	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12034724	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12043726	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13375787	0.85[CHB][hapmap]
rs1359750	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1581870	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2032969	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs28374065	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28445096	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28515016	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28563168	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28575168	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28719150	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28740807	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28804147	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28810187	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3806161	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3819946	0.81[GIH][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3819947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4650004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4650007	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4650287	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4650288	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58715708	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60292279	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6681874	0.85[EUR][1000 genomes]
rs745108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7535692	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7540514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs768223	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9647	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11487952	TYW3	cis	Heart Left Ventricle	GTEx
rs11487952	TYW3	cis	Artery Tibial	GTEx
rs11487952	CRYZ	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
2	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
4	chr1:75175400-75196000	Weak transcription	HSMMtube	muscle
5	chr1:75180000-75196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:75180400-75197200	Weak transcription	Psoas Muscle	Psoas
7	chr1:75183000-75198400	Weak transcription	Fetal Brain Male	brain
8	chr1:75187400-75197200	Weak transcription	Stomach Mucosa	stomach
9	chr1:75187800-75197200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:75188200-75196000	Weak transcription	HSMM	muscle
11	chr1:75188200-75197200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:75188200-75198000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:75188400-75196800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:75188400-75197200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:75188400-75198000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:75189000-75197200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:75189200-75196400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:75189400-75197200	Weak transcription	Left Ventricle	heart
19	chr1:75189400-75197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:75189600-75197200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:75189600-75197400	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:75189800-75196800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:75190800-75196000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:75191400-75197200	Weak transcription	Primary T cells from cord blood	blood
25	chr1:75192000-75197200	Weak transcription	Right Atrium	heart
26	chr1:75192200-75196600	Weak transcription	Aorta	Aorta
27	chr1:75192200-75197000	Weak transcription	Fetal Lung	lung
28	chr1:75192200-75197200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:75192200-75197200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:75192200-75197200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:75192200-75197200	Weak transcription	Colonic Mucosa	Colon
32	chr1:75192200-75197200	Weak transcription	Lung	lung
33	chr1:75192200-75197200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:75192200-75197400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:75192200-75197600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:75192200-75197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:75192200-75198000	Weak transcription	Gastric	stomach
38	chr1:75192400-75196200	Weak transcription	Fetal Intestine Large	intestine
39	chr1:75192400-75196400	Weak transcription	Fetal Stomach	stomach
40	chr1:75192400-75197200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:75192400-75197200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:75192400-75197200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:75192400-75197200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:75192400-75197200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:75192400-75197200	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:75192400-75197400	Weak transcription	Spleen	Spleen
47	chr1:75192400-75198000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:75192400-75198000	Weak transcription	Fetal Thymus	thymus
49	chr1:75192600-75197600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:75192800-75197600	Weak transcription	Primary B cells from peripheral blood	blood

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