Variant report

Variant	rs6542873
Chromosome Location	chr2:99824965-99824966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10179043	0.85[CEU][hapmap]
rs10190421	0.85[CEU][hapmap]
rs10198056	0.87[ASN][1000 genomes]
rs10201856	0.82[CHB][hapmap]
rs11123761	0.93[CHD][hapmap]
rs11689265	0.86[CHD][hapmap]
rs11692699	0.93[CHD][hapmap]
rs11695379	0.93[CHD][hapmap]
rs11695751	0.86[CHD][hapmap]
rs11885942	0.82[CEU][hapmap]
rs11897712	1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12053372	1.00[CEU][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12466388	0.89[EUR][1000 genomes]
rs12468807	0.84[CEU][hapmap]
rs12474833	0.92[EUR][1000 genomes]
rs12475034	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12477438	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428547	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs1349778	0.85[CEU][hapmap]
rs1349779	0.85[CEU][hapmap]
rs13798	0.93[CHD][hapmap]
rs1563107	0.85[CEU][hapmap]
rs1563108	0.85[CEU][hapmap]
rs1580068	0.85[CEU][hapmap]
rs17708218	0.85[CEU][hapmap];0.93[CHD][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs17760953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922624	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1968916	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1993230	0.85[CEU][hapmap]
rs2045057	0.85[CEU][hapmap];0.93[CHD][hapmap];0.81[TSI][hapmap]
rs2171359	0.93[CHD][hapmap]
rs2309524	0.85[CEU][hapmap];0.93[CHD][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2309581	0.93[CHD][hapmap]
rs2516829	0.93[CHD][hapmap]
rs2632277	0.85[CHD][hapmap]
rs3851334	0.92[EUR][1000 genomes]
rs4588238	0.93[CHD][hapmap]
rs4851184	0.85[CEU][hapmap]
rs4851187	0.86[CHD][hapmap]
rs4851196	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57846982	0.82[EUR][1000 genomes]
rs58206803	0.88[EUR][1000 genomes]
rs62153764	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6542864	0.93[CHD][hapmap]
rs6704766	0.85[CEU][hapmap]
rs6708576	0.93[CHD][hapmap]
rs6717729	0.93[CHD][hapmap]
rs6732980	0.84[EUR][1000 genomes]
rs6754843	0.80[CEU][hapmap]
rs6756880	0.80[CEU][hapmap]
rs6757019	0.85[CEU][hapmap]
rs7349217	0.93[CHD][hapmap]
rs73963398	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8179690	0.93[CHD][hapmap]
rs896886	0.85[CEU][hapmap];0.93[CHD][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs9308816	0.85[CEU][hapmap];0.93[CHD][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs972768	0.85[CEU][hapmap]
rs9808541	0.85[CEU][hapmap]
rs995617	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][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	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6542873	LIPT1	cis	parietal	SCAN
rs6542873	LIPT1	cis	multi-tissue	Pritchard
rs6542873	TSGA10	cis	multi-tissue	Pritchard
rs6542873	FAHD2B	cis	parietal	SCAN
rs6542873	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6542873	TSGA10	cis	cerebellum	SCAN
rs6542873	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs6542873	LIPT1	cis	cerebellum	SCAN
rs6542873	TSGA10	cis	parietal	SCAN
rs6542873	LOC129530	cis	multi-tissue	Pritchard
rs6542873	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs6542873	MITD1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
2	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
3	chr2:99803800-99829600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:99807000-99832600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:99807600-99825000	Weak transcription	Stomach Mucosa	stomach
6	chr2:99814000-99834800	Weak transcription	Gastric	stomach
7	chr2:99814200-99828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:99814200-99832400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:99814400-99842200	Weak transcription	Ovary	ovary
10	chr2:99814400-99842800	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:99814800-99840600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:99815000-99829000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:99815000-99834400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:99815000-99836400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:99815000-99840600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:99815000-99840800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:99815000-99841800	Weak transcription	Pancreas	Pancrea
18	chr2:99815000-99842400	Weak transcription	Fetal Lung	lung
19	chr2:99815200-99827400	Weak transcription	HMEC	breast
20	chr2:99815200-99827600	Weak transcription	Brain Germinal Matrix	brain
21	chr2:99815200-99827600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:99815200-99830400	Weak transcription	Brain Anterior Caudate	brain
23	chr2:99815200-99833200	Weak transcription	Lung	lung
24	chr2:99815200-99838400	Weak transcription	Adipose Nuclei	Adipose
25	chr2:99815200-99840600	Weak transcription	Aorta	Aorta
26	chr2:99815200-99841800	Weak transcription	Spleen	Spleen
27	chr2:99815200-99842000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:99815200-99842400	Weak transcription	Brain Substantia Nigra	brain
29	chr2:99815400-99834400	Weak transcription	NHEK	skin
30	chr2:99815400-99834600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:99815600-99834400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:99815600-99834800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:99815600-99842000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr2:99815600-99842200	Weak transcription	Fetal Stomach	stomach
35	chr2:99815600-99843400	Weak transcription	Fetal Brain Female	brain
36	chr2:99818200-99854600	Weak transcription	Left Ventricle	heart
37	chr2:99818400-99827600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:99818400-99830400	Weak transcription	A549	lung
39	chr2:99818400-99836400	Weak transcription	Brain Angular Gyrus	brain
40	chr2:99818600-99842200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:99818800-99827600	Weak transcription	Primary T cells from cord blood	blood
42	chr2:99818800-99843600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:99819000-99843200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:99822200-99830000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:99823200-99830800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:99823400-99826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:99823400-99829400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:99824200-99825200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:99824200-99827600	Strong transcription	Fetal Brain Male	brain

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