Variant report

Variant	rs6673833
Chromosome Location	chr1:85875622-85875623
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	chr1:85872823..85874492-chr1:85874813..85877121,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10493764	0.95[CEU][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402128	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13373844	0.91[ASW][hapmap];0.90[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs1523993	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17387935	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17389112	0.81[ASW][hapmap];0.81[CEU][hapmap];0.91[GIH][hapmap]
rs17590006	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs35092233	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35294786	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35876501	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35956189	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36062892	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3768226	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4475804	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs527762	0.88[GIH][hapmap]
rs61769490	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61783046	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659486	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669293	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7540393	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7555486	0.90[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6673833	SYDE2	cis	cerebellum	SCAN
rs6673833	BCL10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85864800-85876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:85871400-85878400	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:85871600-85876600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:85871800-85877000	Weak transcription	Ovary	ovary
5	chr1:85872000-85877200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:85873200-85876000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:85873200-85879600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:85873400-85876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:85873400-85876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:85873400-85882800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:85873600-85885000	Weak transcription	Fetal Intestine Large	intestine
12	chr1:85873800-85876600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:85873800-85876800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:85873800-85882000	Weak transcription	Fetal Intestine Small	intestine
15	chr1:85873800-85885400	Weak transcription	Fetal Stomach	stomach
16	chr1:85873800-85887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:85874000-85876600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:85874000-85876800	Weak transcription	HSMM	muscle
19	chr1:85874000-85877000	Weak transcription	NHDF-Ad	bronchial
20	chr1:85874000-85877400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:85874000-85878000	Weak transcription	Stomach Mucosa	stomach
22	chr1:85874000-85903800	Weak transcription	NHLF	lung
23	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:85874400-85877000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:85874400-85903600	Weak transcription	HepG2	liver
26	chr1:85874400-85904200	Weak transcription	NH-A	brain
27	chr1:85874600-85876000	Enhancers	Pancreas	Pancrea
28	chr1:85874600-85876600	Weak transcription	HSMMtube	muscle
29	chr1:85874600-85877200	Weak transcription	Aorta	Aorta
30	chr1:85874800-85877000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:85875000-85876400	Weak transcription	Osteobl	bone
32	chr1:85875000-85877000	Weak transcription	HUVEC	blood vessel
33	chr1:85875000-85882800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:85875200-85876600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:85875200-85877400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:85875400-85876600	Weak transcription	Liver	Liver
37	chr1:85875400-85877200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:85875400-85877400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:85875400-85878800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:85875400-85880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:85875400-85885600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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