Variant report

Variant	rs1628249
Chromosome Location	chr9:103356112-103356113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103348301..103352050-chr9:103353631..103357839,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12002878	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12005789	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1226587	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226589	0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs1226590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226592	0.81[ASW][hapmap];0.82[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1226593	0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs1226595	0.81[AMR][1000 genomes]
rs1236813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17742370	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1780020	0.81[AMR][1000 genomes]
rs2151597	0.81[ASW][hapmap];0.82[CEU][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2184201	0.81[AMR][1000 genomes]
rs2780954	1.00[ASN][1000 genomes]
rs2780955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800282	0.83[AMR][1000 genomes]
rs2800283	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2800284	0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs2800285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800289	1.00[ASN][1000 genomes]
rs2800290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57290629	0.95[ASN][1000 genomes]
rs60422299	0.95[ASN][1000 genomes]
rs951868	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv893624	chr9:103351931-103416553	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1628249	C9orf21	cis	cerebellum	SCAN
rs1628249	CTSL2	cis	parietal	SCAN
rs1628249	TMEFF1	cis	parietal	SCAN
rs1628249	GPT2	trans	parietal	SCAN
rs1628249	MURC	cis	Muscle Skeletal	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103329600-103360800	Weak transcription	Aorta	Aorta
2	chr9:103330000-103357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:103331600-103360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:103332400-103357600	Weak transcription	Fetal Lung	lung
5	chr9:103333600-103360800	Weak transcription	Fetal Brain Male	brain
6	chr9:103343200-103360600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:103346200-103359800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:103348600-103361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:103348800-103360600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:103349600-103360800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:103349800-103359400	Weak transcription	Brain Germinal Matrix	brain
12	chr9:103350000-103357600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:103350000-103357600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:103350000-103360200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:103350200-103357600	Weak transcription	Fetal Brain Female	brain
16	chr9:103350200-103360200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:103350400-103357600	Weak transcription	Hela-S3	cervix
18	chr9:103350400-103359200	Weak transcription	Fetal Heart	heart
19	chr9:103350400-103360000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:103350600-103360800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:103350800-103357600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:103351000-103360000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:103351000-103360600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:103351200-103357600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:103351600-103360600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:103352200-103357800	Weak transcription	A549	lung
27	chr9:103353200-103357600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:103353200-103357600	Weak transcription	HUVEC	blood vessel
29	chr9:103353400-103360600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:103353600-103356400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr9:103353600-103356400	Weak transcription	NHDF-Ad	bronchial
32	chr9:103353600-103357600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:103353600-103360400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:103353800-103357600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:103353800-103357600	Weak transcription	Brain Anterior Caudate	brain
36	chr9:103353800-103357800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:103353800-103357800	Weak transcription	NH-A	brain
38	chr9:103353800-103357800	Weak transcription	Osteobl	bone
39	chr9:103354000-103357600	Weak transcription	Fetal Muscle Leg	muscle
40	chr9:103354000-103357600	Weak transcription	HSMM	muscle
41	chr9:103354000-103357600	Weak transcription	HSMMtube	muscle
42	chr9:103354000-103360800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:103354200-103357400	Weak transcription	Brain Angular Gyrus	brain
44	chr9:103354200-103357600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:103354400-103359600	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:103354400-103360800	Weak transcription	Brain Substantia Nigra	brain
47	chr9:103354600-103357600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr9:103354600-103357600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:103354600-103360800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:103354800-103357600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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