Variant report

Variant	rs12082330
Chromosome Location	chr1:67489064-67489065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10489633	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074265	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208977	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11208980	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11208986	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11208987	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11208988	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11208989	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11208990	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11208993	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12059957	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12060891	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12061148	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12062086	0.87[ASN][1000 genomes]
rs12073258	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12074407	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12079643	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12082503	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090955	0.82[CHB][hapmap]
rs12091194	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17097312	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17129589	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17129592	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17129595	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17129627	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2985809	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs3924795	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3924796	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs41356950	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4553158	0.82[CHB][hapmap]
rs56774527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57476475	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58083543	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58096117	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58465390	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6588226	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6588231	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6588232	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6588234	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681625	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6698599	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67073063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67471683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517647	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520341	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524757	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7528485	0.88[CEU][hapmap]
rs7538922	0.87[ASN][1000 genomes]
rs7551021	0.82[CHB][hapmap];1.00[JPT][hapmap]

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	nsv461751	chr1:67479598-67689036	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv546445	chr1:67479598-67689036	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12082330	SLC35D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67449400-67501800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:67451200-67506200	Weak transcription	Hela-S3	cervix
3	chr1:67455200-67495000	Weak transcription	Small Intestine	intestine
4	chr1:67455400-67509400	Weak transcription	Spleen	Spleen
5	chr1:67462400-67508400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:67465200-67502400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:67465200-67506400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:67468600-67501800	Weak transcription	Psoas Muscle	Psoas
9	chr1:67470800-67505400	Weak transcription	Gastric	stomach
10	chr1:67471800-67503800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:67472400-67502400	Weak transcription	Fetal Brain Male	brain
12	chr1:67473800-67518000	Weak transcription	A549	lung
13	chr1:67474600-67500800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:67476000-67504600	Weak transcription	Lung	lung
15	chr1:67476000-67508400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:67478000-67508800	Weak transcription	Colonic Mucosa	Colon
17	chr1:67479800-67503200	Weak transcription	K562	blood
18	chr1:67480800-67489200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:67481000-67490600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:67482600-67491000	Strong transcription	Primary T cells from cord blood	blood
21	chr1:67482600-67498800	Strong transcription	Fetal Intestine Large	intestine
22	chr1:67484000-67490800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:67484000-67518400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:67484200-67489200	Strong transcription	Fetal Lung	lung
25	chr1:67484600-67490400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:67484800-67501800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:67485400-67490400	Weak transcription	Pancreas	Pancrea
28	chr1:67485400-67503600	Weak transcription	Ovary	ovary
29	chr1:67485400-67504000	Weak transcription	Brain Anterior Caudate	brain
30	chr1:67485400-67505800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:67485600-67489800	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:67485600-67503000	Weak transcription	Placenta	Placenta
33	chr1:67485800-67490000	Weak transcription	HSMMtube	muscle
34	chr1:67485800-67490400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:67485800-67503000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:67485800-67504600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:67485800-67506200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:67485800-67507600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:67486000-67489200	Weak transcription	Fetal Intestine Small	intestine
40	chr1:67486000-67501600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:67486000-67509600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:67486200-67516800	Weak transcription	NHEK	skin
43	chr1:67486600-67494800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:67486600-67500400	Weak transcription	GM12878-XiMat	blood
45	chr1:67486600-67501800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:67486600-67501800	Weak transcription	Fetal Kidney	kidney
47	chr1:67486600-67502000	Weak transcription	Brain Germinal Matrix	brain
48	chr1:67486800-67489200	Strong transcription	HSMM	muscle
49	chr1:67486800-67495000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:67486800-67495800	Weak transcription	Stomach Smooth Muscle	stomach

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