Variant report

Variant	rs12750321
Chromosome Location	chr1:154251626-154251627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10158820	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1044013	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11265122	0.81[JPT][hapmap]
rs11265238	0.90[JPT][hapmap]
rs11265251	0.95[JPT][hapmap]
rs11265425	0.90[JPT][hapmap]
rs11802893	0.81[JPT][hapmap]
rs1194593	0.96[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1194596	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12023901	0.88[ASN][1000 genomes]
rs12025237	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs12026177	0.90[JPT][hapmap]
rs12026475	0.81[JPT][hapmap]
rs12026615	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs12027999	0.88[ASN][1000 genomes]
rs12028949	0.90[JPT][hapmap]
rs12062977	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs12135346	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12405309	0.82[JPT][hapmap]
rs12733060	0.89[ASN][1000 genomes]
rs12738393	0.89[ASN][1000 genomes]
rs12742691	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12743874	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749447	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16835846	0.86[JPT][hapmap]
rs1760801	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1760802	0.96[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1760803	0.82[ASN][1000 genomes]
rs2274993	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2282227	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2340473	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2790689	0.80[JPT][hapmap]
rs2879788	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3762340	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3790613	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3790614	0.89[ASN][1000 genomes]
rs3811453	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3811455	0.90[JPT][hapmap]
rs3828077	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs3935419	0.90[JPT][hapmap]
rs4459102	0.80[JPT][hapmap]
rs4521985	0.81[JPT][hapmap]
rs4620534	0.90[JPT][hapmap]
rs4845363	0.81[JPT][hapmap]
rs4845597	0.81[JPT][hapmap]
rs4845600	0.81[JPT][hapmap]
rs4845601	0.81[JPT][hapmap]
rs6427509	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6659053	0.81[JPT][hapmap]
rs6667928	0.81[JPT][hapmap]
rs6673752	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6678826	0.81[JPT][hapmap]
rs6719	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7522777	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9803857	0.86[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12750321	UBAP2L	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154246200-154259400	Weak transcription	Right Atrium	heart
2	chr1:154246600-154253400	Weak transcription	HepG2	liver
3	chr1:154248000-154252600	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:154248200-154252000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:154248200-154252000	Weak transcription	Brain Germinal Matrix	brain
6	chr1:154248200-154252000	Weak transcription	Colonic Mucosa	Colon
7	chr1:154248200-154252000	Weak transcription	Esophagus	oesophagus
8	chr1:154248200-154252200	Weak transcription	Brain Anterior Caudate	brain
9	chr1:154248200-154252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:154248200-154255200	Weak transcription	Pancreas	Pancrea
11	chr1:154248400-154252200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:154248400-154252200	Weak transcription	Left Ventricle	heart
13	chr1:154248400-154252200	Weak transcription	Psoas Muscle	Psoas
14	chr1:154248400-154252400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:154248400-154252400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:154248400-154252400	Weak transcription	Brain Angular Gyrus	brain
17	chr1:154248400-154252400	Weak transcription	Thymus	Thymus
18	chr1:154248400-154252600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:154248400-154253200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:154248400-154255000	Weak transcription	A549	lung
21	chr1:154248400-154255800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:154248400-154256800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:154248400-154261000	Weak transcription	K562	blood
24	chr1:154248600-154252000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:154248600-154252000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:154248600-154252600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:154248600-154252600	Weak transcription	Fetal Brain Female	brain
28	chr1:154249000-154252200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:154249200-154252200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:154249200-154252200	Weak transcription	Right Ventricle	heart
31	chr1:154249200-154252600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:154249400-154252000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:154249400-154252400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:154249400-154252400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:154249400-154252800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:154249400-154252800	Weak transcription	Fetal Intestine Large	intestine
37	chr1:154249400-154255000	Weak transcription	Spleen	Spleen
38	chr1:154249600-154252000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:154249600-154252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:154249600-154252200	Weak transcription	Liver	Liver
41	chr1:154249600-154252200	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:154249600-154252400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:154249600-154252400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:154249600-154254000	Weak transcription	Ovary	ovary
45	chr1:154249600-154255000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:154250600-154252200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:154250600-154253200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:154250800-154252400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:154250800-154252400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:154250800-154252600	Weak transcription	Fetal Intestine Small	intestine

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