Variant report

Variant	rs10489339
Chromosome Location	chr1:209781828-209781829
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	chr1:209749053..209751120-chr1:209781399..209783226,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17014768	0.80[TSI][hapmap]
rs17014820	0.87[CHD][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs17014830	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs17014836	1.00[CHB][hapmap]
rs17014866	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55967608	0.82[AFR][1000 genomes]
rs6658827	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs742253	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs7516885	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.84[AFR][1000 genomes]
rs880782	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs880783	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10489339	SLC30A1	cis	cerebellum	SCAN
rs10489339	C1orf97	cis	parietal	SCAN
rs10489339	TMCC2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209764600-209791200	Weak transcription	Brain Anterior Caudate	brain
2	chr1:209771000-209787600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:209772200-209783000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:209775600-209791400	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:209775800-209789800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:209776000-209790200	Weak transcription	Brain Germinal Matrix	brain
7	chr1:209776000-209791000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:209777800-209793000	Weak transcription	Ovary	ovary
9	chr1:209777800-209796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:209778400-209791400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:209779400-209785800	Weak transcription	Fetal Stomach	stomach
12	chr1:209779600-209793400	Weak transcription	Thymus	Thymus
13	chr1:209780200-209784000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:209780800-209791800	Weak transcription	Fetal Brain Male	brain
15	chr1:209781000-209782800	Weak transcription	HSMMtube	muscle
16	chr1:209781200-209782400	Strong transcription	Spleen	Spleen
17	chr1:209781200-209784600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:209781200-209785400	Weak transcription	Fetal Intestine Small	intestine
19	chr1:209781200-209786400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:209781200-209791800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:209781400-209782800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:209781400-209787000	Weak transcription	Fetal Intestine Large	intestine
23	chr1:209781400-209789200	Weak transcription	Right Atrium	heart
24	chr1:209781600-209783200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:209781600-209783200	Weak transcription	Fetal Heart	heart
26	chr1:209781600-209793600	Weak transcription	Esophagus	oesophagus
27	chr1:209781600-209793600	Weak transcription	Fetal Lung	lung
28	chr1:209781800-209782800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:209781800-209783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:209781800-209785000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:209781800-209786200	Weak transcription	HMEC	breast
32	chr1:209781800-209786800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:209781800-209787000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:209781800-209787400	Weak transcription	NHEK	skin
35	chr1:209781800-209788000	Weak transcription	Gastric	stomach

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