Variant report

Variant	rs2273779
Chromosome Location	chr1:186273994-186273995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:186253069..186255534-chr1:186273980..186275987,2	K562	blood:
2	chr1:186263956..186266489-chr1:186272797..186275171,2	MCF-7	breast:
3	chr1:186267939..186270683-chr1:186273055..186275696,2	K562	blood:
4	chr1:186268258..186271597-chr1:186273909..186276929,3	MCF-7	breast:
5	chr1:186272061..186274014-chr1:186281964..186283567,2	K562	blood:

Variant related genes	Relation type
ENSG00000116690	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1003127	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10911847	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911849	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911854	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911858	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11582844	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12064371	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068740	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs12069419	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078527	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12082399	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12084264	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12085497	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12093440	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1547084	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17580052	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037959	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2383479	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2383480	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3737940	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]
rs3753564	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753567	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61810289	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61810292	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61831150	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61831151	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519719	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539128	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2273779	C1orf27	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

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	chr1:186269000-186274800	Weak transcription	Psoas Muscle	Psoas
7	chr1:186269000-186281400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:186269400-186277600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:186269400-186281400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:186269400-186281400	Weak transcription	Fetal Heart	heart
11	chr1:186270200-186277400	Enhancers	Primary T cells from cord blood	blood
12	chr1:186270200-186277800	Enhancers	Fetal Thymus	thymus
13	chr1:186270400-186279200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:186270400-186279600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:186271200-186276200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:186271400-186276800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:186271800-186277200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:186271800-186278200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:186272000-186277600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:186272000-186280000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:186272000-186280000	Weak transcription	Osteobl	bone
22	chr1:186272000-186306000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:186272400-186277600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:186272400-186278800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:186272400-186279600	Strong transcription	Liver	Liver
26	chr1:186272400-186280400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:186272400-186281200	Weak transcription	NHDF-Ad	bronchial
28	chr1:186273200-186274600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:186273200-186283800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:186273200-186284000	Weak transcription	Spleen	Spleen
31	chr1:186273200-186286200	Weak transcription	Pancreas	Pancrea
32	chr1:186273200-186290000	Weak transcription	Gastric	stomach
33	chr1:186273400-186274000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:186273400-186274800	Weak transcription	Thymus	Thymus
35	chr1:186273600-186276400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:186273800-186277400	Enhancers	Primary T helper cells PMA-I stimulated	--

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