Variant report

Variant	rs1487271
Chromosome Location	chr2:99831671-99831672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10180688	0.89[CEU][hapmap]
rs10187854	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10865030	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11123769	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123776	0.87[EUR][1000 genomes]
rs11123778	0.85[EUR][1000 genomes]
rs11123784	0.89[CEU][hapmap]
rs11525712	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12328219	1.00[ASN][1000 genomes]
rs12617324	0.81[EUR][1000 genomes]
rs12623835	0.88[CEU][hapmap]
rs12992356	0.82[CEU][hapmap]
rs12993310	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022798	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13028722	0.89[CEU][hapmap]
rs13032885	0.87[EUR][1000 genomes]
rs13384665	0.80[ASN][1000 genomes]
rs13393060	1.00[ASN][1000 genomes]
rs13401163	0.89[CEU][hapmap]
rs13404012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13430662	0.80[ASN][1000 genomes]
rs1487272	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1565054	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1843807	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882598	0.89[CEU][hapmap]
rs1922625	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1922627	0.89[EUR][1000 genomes]
rs1948101	0.89[EUR][1000 genomes]
rs2091798	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309577	0.89[CEU][hapmap]
rs2309615	0.87[EUR][1000 genomes]
rs2309616	0.89[EUR][1000 genomes]
rs2632285	0.81[EUR][1000 genomes]
rs28745279	0.80[ASN][1000 genomes]
rs35996174	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3828162	0.88[CEU][hapmap]
rs4522654	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs4850896	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs4851189	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4851191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851197	0.85[EUR][1000 genomes]
rs4851199	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs6542871	0.93[EUR][1000 genomes]
rs6542877	0.87[EUR][1000 genomes]
rs6712137	0.89[CEU][hapmap]
rs6726711	0.89[CEU][hapmap]
rs6728723	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6744199	0.84[EUR][1000 genomes]
rs6745645	0.83[EUR][1000 genomes]
rs6747601	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6749029	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7567230	0.87[EUR][1000 genomes]
rs7567462	0.89[EUR][1000 genomes]
rs7569805	0.89[CEU][hapmap]
rs7579143	0.88[CEU][hapmap]
rs7579171	0.85[EUR][1000 genomes]
rs7579999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581337	0.87[EUR][1000 genomes]
rs7584022	0.81[EUR][1000 genomes]
rs7584705	0.87[EUR][1000 genomes]
rs7586635	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7599384	0.89[CEU][hapmap]
rs7599843	0.89[EUR][1000 genomes]
rs7602401	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602637	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7603388	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7606279	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs896884	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9308819	0.88[CEU][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv515702	chr2:99827733-99922967	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv458685	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv582519	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv963164	chr2:99829782-99832972	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1487271	LYG1	cis	Whole Blood	GTEx
rs1487271	TSGA10	cis	Thyroid	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
2	chr2:99807000-99832600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:99814000-99834800	Weak transcription	Gastric	stomach
4	chr2:99814200-99832400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:99814400-99842200	Weak transcription	Ovary	ovary
6	chr2:99814400-99842800	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:99814800-99840600	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:99815000-99834400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:99815000-99836400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:99815000-99840600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:99815000-99840800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:99815000-99841800	Weak transcription	Pancreas	Pancrea
13	chr2:99815000-99842400	Weak transcription	Fetal Lung	lung
14	chr2:99815200-99833200	Weak transcription	Lung	lung
15	chr2:99815200-99838400	Weak transcription	Adipose Nuclei	Adipose
16	chr2:99815200-99840600	Weak transcription	Aorta	Aorta
17	chr2:99815200-99841800	Weak transcription	Spleen	Spleen
18	chr2:99815200-99842000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:99815200-99842400	Weak transcription	Brain Substantia Nigra	brain
20	chr2:99815400-99834400	Weak transcription	NHEK	skin
21	chr2:99815400-99834600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:99815600-99834400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:99815600-99834800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:99815600-99842000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:99815600-99842200	Weak transcription	Fetal Stomach	stomach
26	chr2:99815600-99843400	Weak transcription	Fetal Brain Female	brain
27	chr2:99818200-99854600	Weak transcription	Left Ventricle	heart
28	chr2:99818400-99836400	Weak transcription	Brain Angular Gyrus	brain
29	chr2:99818600-99842200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:99818800-99843600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:99819000-99843200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:99825200-99843200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:99825400-99841800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:99826400-99834400	Weak transcription	Fetal Intestine Small	intestine
35	chr2:99827600-99832600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:99827600-99842800	Weak transcription	Fetal Brain Male	brain
37	chr2:99828000-99837400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:99828200-99832000	Weak transcription	Brain Germinal Matrix	brain
39	chr2:99828200-99835600	Weak transcription	HepG2	liver
40	chr2:99828600-99839400	Weak transcription	Primary T cells from cord blood	blood
41	chr2:99829600-99844400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:99830400-99834400	Weak transcription	Dnd41	blood
43	chr2:99830600-99832000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:99831200-99837000	Weak transcription	Fetal Intestine Large	intestine
45	chr2:99831400-99832400	Weak transcription	Brain Anterior Caudate	brain

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