Variant report

Variant	rs12119873
Chromosome Location	chr1:85067560-85067561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85062635..85064532-chr1:85066699..85068510,2	K562	blood:
2	chr1:85066761..85068323-chr1:85074286..85076322,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10493752	1.00[JPT][hapmap]
rs11164000	1.00[JPT][hapmap]
rs11164005	0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs12123470	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12127160	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12131448	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12137275	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12141472	0.87[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs12145771	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1417295	0.86[EUR][1000 genomes]
rs1517601	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1517602	1.00[JPT][hapmap]
rs15911	0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1914477	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2303307	0.81[CEU][hapmap]
rs2911594	0.92[EUR][1000 genomes]
rs2911597	0.87[EUR][1000 genomes]
rs2911598	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2911599	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2911607	0.86[EUR][1000 genomes]
rs2911609	0.84[EUR][1000 genomes]
rs2943671	0.85[EUR][1000 genomes]
rs2945143	0.86[EUR][1000 genomes]
rs2945145	0.94[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs2945147	0.94[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs2994934	0.84[EUR][1000 genomes]
rs2994935	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2994937	0.87[EUR][1000 genomes]
rs2994938	0.87[EUR][1000 genomes]
rs2994948	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4356070	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4907080	1.00[JPT][hapmap]
rs7517756	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12119873	BCL10	cis	cerebellum	SCAN
rs12119873	SPATA1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85051000-85069800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:85065600-85068200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:85065600-85068200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:85065600-85068800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:85065600-85069600	Weak transcription	Left Ventricle	heart
6	chr1:85065800-85068000	Weak transcription	Aorta	Aorta
7	chr1:85065800-85068000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:85065800-85069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:85065800-85069000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:85066000-85068800	Weak transcription	HMEC	breast
11	chr1:85066000-85068800	Weak transcription	NHEK	skin
12	chr1:85066000-85069000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:85066000-85069000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:85066200-85068000	Weak transcription	Fetal Heart	heart
15	chr1:85066200-85068600	Weak transcription	HSMMtube	muscle
16	chr1:85066200-85069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:85066400-85068400	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:85066400-85068400	Weak transcription	Hela-S3	cervix
19	chr1:85066400-85068600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:85066400-85068600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:85066400-85069000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:85066600-85067600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:85066600-85067800	Weak transcription	NHDF-Ad	bronchial
24	chr1:85066600-85068400	Weak transcription	NH-A	brain
25	chr1:85066600-85068600	Weak transcription	HSMM	muscle
26	chr1:85066600-85069000	Weak transcription	NHLF	lung
27	chr1:85066800-85068000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:85066800-85068400	Weak transcription	Osteobl	bone
29	chr1:85067000-85067600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:85067000-85068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:85067000-85068000	Weak transcription	HUVEC	blood vessel
32	chr1:85067000-85068200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:85067000-85068600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:85067200-85068600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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