Variant report

Variant	rs3737940
Chromosome Location	chr1:186277989-186277990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1003127	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10911847	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911849	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911854	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911858	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11582844	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12064371	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12068740	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[YRI][hapmap]
rs12069419	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12078527	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12082399	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12084264	0.87[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12085497	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12093440	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1547084	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17580052	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2037959	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178214	0.84[AFR][1000 genomes]
rs2273779	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2383479	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2383480	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3753564	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3753567	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61810289	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61810292	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61831150	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61831151	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519719	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539128	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3343276	chr1:186275179-186278377	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3737940	C1orf27	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186265600-186279400	Weak transcription	A549	lung
2	chr1:186267200-186281600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:186267400-186280400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:186268400-186279200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr1:186268600-186281200	Weak transcription	Fetal Intestine Large	intestine
6	chr1:186269000-186281400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:186269400-186281400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:186269400-186281400	Weak transcription	Fetal Heart	heart
9	chr1:186270400-186279200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:186270400-186279600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:186271800-186278200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:186272000-186280000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:186272000-186280000	Weak transcription	Osteobl	bone
14	chr1:186272000-186306000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:186272400-186278800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:186272400-186279600	Strong transcription	Liver	Liver
17	chr1:186272400-186280400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:186272400-186281200	Weak transcription	NHDF-Ad	bronchial
19	chr1:186273200-186283800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:186273200-186284000	Weak transcription	Spleen	Spleen
21	chr1:186273200-186286200	Weak transcription	Pancreas	Pancrea
22	chr1:186273200-186290000	Weak transcription	Gastric	stomach
23	chr1:186274600-186278200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:186274800-186278000	Enhancers	Thymus	Thymus
25	chr1:186275000-186279600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:186275000-186279600	Weak transcription	Left Ventricle	heart
27	chr1:186275000-186280200	Weak transcription	Placenta	Placenta
28	chr1:186275000-186281200	Weak transcription	Adipose Nuclei	Adipose
29	chr1:186275000-186281400	Weak transcription	NHEK	skin
30	chr1:186275000-186282800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:186275000-186284000	Weak transcription	Aorta	Aorta
32	chr1:186275000-186284000	Weak transcription	Esophagus	oesophagus
33	chr1:186275000-186284000	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:186275000-186284000	Weak transcription	Lung	lung
35	chr1:186275000-186284000	Weak transcription	Right Ventricle	heart
36	chr1:186275000-186284800	Weak transcription	Brain Substantia Nigra	brain
37	chr1:186275000-186286200	Weak transcription	Psoas Muscle	Psoas
38	chr1:186275200-186281200	Weak transcription	HUVEC	blood vessel
39	chr1:186275200-186281400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:186275200-186284000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:186275600-186283600	Weak transcription	HSMMtube	muscle
42	chr1:186276400-186280600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:186276400-186281800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:186276600-186278200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:186276600-186280400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:186276600-186280800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:186276600-186281400	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:186276600-186281600	Weak transcription	Brain Angular Gyrus	brain
49	chr1:186276800-186278200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:186276800-186278400	Weak transcription	Monocytes-CD14+_RO01746	blood

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