Variant report

Variant	rs1226592
Chromosome Location	chr9:103339947-103339948
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10989168	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1135455	0.98[ASN][1000 genomes]
rs1226587	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1226588	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1226590	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1226591	0.81[ASW][hapmap];0.82[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1226594	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1226596	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1236813	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13291670	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13301089	0.95[ASN][1000 genomes]
rs1628249	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1760290	0.97[ASN][1000 genomes]
rs2151597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2489363	0.98[ASN][1000 genomes]
rs2489364	1.00[ASN][1000 genomes]
rs2780955	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2780956	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2780958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2780959	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2780960	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2800280	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2800281	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2800285	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2800288	0.97[ASN][1000 genomes]
rs2800290	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72735191	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1226592	CTSL2	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
2	chr9:103307400-103341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:103307400-103347800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:103308000-103340200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:103308600-103345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:103311800-103342400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:103313200-103340800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:103318400-103342400	Weak transcription	Brain Anterior Caudate	brain
9	chr9:103318600-103344000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:103322400-103340400	Weak transcription	Brain Substantia Nigra	brain
11	chr9:103322600-103341800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:103323000-103340200	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:103323400-103342000	Weak transcription	Brain Angular Gyrus	brain
14	chr9:103323800-103340600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:103324000-103340200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:103324800-103345400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:103327800-103349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:103329600-103360800	Weak transcription	Aorta	Aorta
19	chr9:103329800-103351800	Weak transcription	Ovary	ovary
20	chr9:103330000-103357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:103330400-103345400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:103330400-103351600	Weak transcription	Fetal Stomach	stomach
23	chr9:103330800-103349400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:103331600-103360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:103332400-103351600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:103332400-103357600	Weak transcription	Fetal Lung	lung
27	chr9:103333600-103360800	Weak transcription	Fetal Brain Male	brain
28	chr9:103334200-103341200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:103334200-103351000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:103334600-103350600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:103334800-103350200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:103335000-103351000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:103335400-103341400	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr9:103335600-103341200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:103336400-103340200	Enhancers	HSMM	muscle
36	chr9:103336800-103347800	Weak transcription	Brain Germinal Matrix	brain
37	chr9:103337400-103342800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:103337600-103340000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:103337600-103340600	Enhancers	NHLF	lung
40	chr9:103337600-103352200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:103338400-103340200	Weak transcription	Fetal Brain Female	brain
42	chr9:103338600-103340000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:103338600-103340000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr9:103338600-103340000	Weak transcription	Fetal Muscle Leg	muscle
45	chr9:103338600-103340000	Enhancers	HSMMtube	muscle
46	chr9:103338600-103340000	Weak transcription	NH-A	brain
47	chr9:103338600-103340200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:103338600-103340200	Weak transcription	Psoas Muscle	Psoas
49	chr9:103338600-103340400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:103338600-103348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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