Variant report

Variant	rs7538839
Chromosome Location	chr1:171877867-171877868
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1015009	0.90[ASN][1000 genomes]
rs1015010	0.90[ASN][1000 genomes]
rs10436867	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737340	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs10798687	0.90[ASN][1000 genomes]
rs10798688	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10798690	0.90[ASN][1000 genomes]
rs10798691	0.90[ASN][1000 genomes]
rs10798692	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10798693	0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10798712	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798751	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs10913811	0.90[ASN][1000 genomes]
rs10913812	0.90[ASN][1000 genomes]
rs10913814	0.90[ASN][1000 genomes]
rs11579330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12028585	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048200	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1555384	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145382	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs2294723	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2294724	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2901603	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs6425438	0.92[CEU][hapmap]
rs6425481	0.86[CHB][hapmap]
rs6425482	0.86[CHB][hapmap]
rs72711798	0.81[ASN][1000 genomes]
rs72713710	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72713711	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518914	0.86[CHB][hapmap]
rs7546406	0.94[EUR][1000 genomes];0.97[ASN][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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7538839	RC3H1	cis	cerebellum	SCAN
rs7538839	MYOC	cis	parietal	SCAN
rs7538839	DNM3	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171862200-171882600	Weak transcription	Aorta	Aorta
2	chr1:171868600-171880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:171868800-171878000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:171868800-171884000	Weak transcription	Fetal Lung	lung
5	chr1:171868800-171885000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:171869400-171879400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:171870000-171878000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:171871200-171879000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:171871600-171878000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:171872200-171883000	Weak transcription	Lung	lung
11	chr1:171872600-171878000	Weak transcription	Brain Substantia Nigra	brain
12	chr1:171872600-171879400	Weak transcription	NHEK	skin
13	chr1:171872600-171879600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:171874000-171878600	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:171874200-171878800	Weak transcription	Brain Angular Gyrus	brain
16	chr1:171874600-171879000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:171874600-171879600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:171874800-171878800	Weak transcription	Brain Anterior Caudate	brain
19	chr1:171875200-171878000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:171876800-171879600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:171877000-171878000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:171877800-171878800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:171877800-171879800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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