Variant report

Variant	rs1150895
Chromosome Location	chr1:227056091-227056092
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	chr1:227045661..227048469-chr1:227054532..227056179,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10799368	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916039	0.91[JPT][hapmap]
rs10916054	0.94[EUR][1000 genomes]
rs11405	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs1150896	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590925	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12039247	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126209	0.92[EUR][1000 genomes]
rs12128150	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130758	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12131495	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133772	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133818	0.91[EUR][1000 genomes]
rs12563993	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12749910	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1295642	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1295645	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295648	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1295651	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1295652	0.81[EUR][1000 genomes]
rs1297990	0.92[CEU][hapmap]
rs1800678	0.92[CEU][hapmap]
rs2236913	0.92[CEU][hapmap]
rs2802267	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2855563	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34741989	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61837761	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61837762	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61837763	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426542	0.88[EUR][1000 genomes]
rs6426543	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426545	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426546	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6660109	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6660716	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6663555	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6678134	0.91[EUR][1000 genomes]
rs743602	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7525811	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7553957	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9660802	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3381082	chr1:227029266-227059927	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1150895	GJC2	cis	parietal	SCAN
rs1150895	LEFTY1	cis	cerebellum	SCAN
rs1150895	PYCR2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227045200-227057800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:227051600-227057800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:227051600-227057800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:227051600-227057800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:227051800-227057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:227051800-227057800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:227051800-227057800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:227051800-227057800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:227051800-227057800	Weak transcription	Osteobl	bone
10	chr1:227052000-227057800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:227052200-227057800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:227052400-227057800	Weak transcription	Pancreas	Pancrea
13	chr1:227053000-227057800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:227053400-227057800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:227053600-227057600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:227053600-227057800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:227053600-227057800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:227053800-227057800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:227053800-227057800	Weak transcription	Liver	Liver
20	chr1:227053800-227057800	Weak transcription	NHDF-Ad	bronchial
21	chr1:227053800-227057800	Weak transcription	NHLF	lung
22	chr1:227053800-227058000	Weak transcription	Gastric	stomach
23	chr1:227054200-227057800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:227054200-227057800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:227054200-227057800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:227054200-227057800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:227054400-227057800	Weak transcription	Right Atrium	heart
28	chr1:227055600-227057200	Weak transcription	Hela-S3	cervix
29	chr1:227055600-227057600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:227055600-227057600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:227055600-227057600	Weak transcription	NHEK	skin
32	chr1:227055600-227057800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:227055600-227057800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:227055600-227057800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:227055600-227057800	Weak transcription	HMEC	breast
36	chr1:227055600-227058200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:227055800-227057800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:227055800-227057800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:227056000-227057600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:227056000-227057600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:227056000-227057800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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