Variant report

Variant	rs7349360
Chromosome Location	chr2:55413644-55413645
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17046778	0.91[ASN][1000 genomes]
rs1821832	0.81[AMR][1000 genomes]
rs2576722	0.83[AMR][1000 genomes]
rs2920965	0.82[ASN][1000 genomes]
rs57529275	0.81[ASN][1000 genomes]
rs57681837	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59439819	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59783675	0.91[AMR][1000 genomes]
rs61109509	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61486882	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6726380	0.88[ASN][1000 genomes]
rs71414550	0.81[AMR][1000 genomes]
rs7349405	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7349360	CLHC1	cis	Muscle Skeletal	GTEx
rs7349360	CLHC1	cis	Esophagus Mucosa	GTEx
rs7349360	CLHC1	cis	Esophagus Muscularis	GTEx
rs7349360	CLHC1	cis	Artery Tibial	GTEx
rs7349360	CLHC1	cis	Whole Blood	GTEx
rs7349360	CLHC1	cis	Thyroid	GTEx
rs7349360	CLHC1	cis	Nerve Tibial	GTEx
rs7349360	C2orf63	cis	multi-tissue	Pritchard
rs7349360	CLHC1	cis	Heart Left Ventricle	GTEx
rs7349360	CLHC1	cis	Artery Aorta	GTEx
rs7349360	CLHC1	cis	lung	GTEx
rs7349360	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs7349360	CLHC1	cis	Stomach	GTEx
rs7349360	CLHC1	cis	Adipose Subcutaneous	GTEx
rs7349360	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
2	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55395600-55422800	Weak transcription	Ovary	ovary
5	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
6	chr2:55395800-55418200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:55395800-55418400	Weak transcription	Fetal Intestine Large	intestine
8	chr2:55395800-55427000	Weak transcription	Aorta	Aorta
9	chr2:55397200-55450000	Weak transcription	NH-A	brain
10	chr2:55397400-55422400	Weak transcription	HSMMtube	muscle
11	chr2:55397400-55423000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:55399600-55419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:55399600-55423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:55399800-55416600	Weak transcription	Primary T cells from cord blood	blood
15	chr2:55401600-55419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:55402600-55422000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:55402600-55423200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
19	chr2:55403200-55423800	Weak transcription	Osteobl	bone
20	chr2:55403200-55426800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:55403200-55431800	Weak transcription	Fetal Brain Male	brain
22	chr2:55403400-55418800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:55403400-55423000	Weak transcription	NHEK	skin
24	chr2:55403600-55416600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:55403600-55420600	Weak transcription	HSMM	muscle
26	chr2:55404200-55423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:55405400-55423000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:55406800-55423000	Weak transcription	Lung	lung
29	chr2:55408600-55423000	Weak transcription	Pancreas	Pancrea
30	chr2:55408800-55423600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:55409000-55423000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:55409200-55416600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:55409200-55425800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:55409400-55418400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:55409600-55418400	Weak transcription	Fetal Stomach	stomach
36	chr2:55409800-55418200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:55410000-55424000	Weak transcription	Fetal Thymus	thymus
38	chr2:55410600-55422800	Weak transcription	HepG2	liver
39	chr2:55411200-55418400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:55411200-55427000	Weak transcription	Primary B cells from cord blood	blood
41	chr2:55411800-55417800	Weak transcription	Fetal Intestine Small	intestine
42	chr2:55412200-55423000	Weak transcription	Dnd41	blood
43	chr2:55412600-55416600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:55412600-55423000	Weak transcription	Thymus	Thymus
45	chr2:55412800-55417400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:55412800-55422000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:55412800-55428200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:55413000-55427000	Weak transcription	Brain Angular Gyrus	brain
49	chr2:55413600-55427000	Weak transcription	Fetal Lung	lung

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