Variant report

Variant	rs6542843
Chromosome Location	chr2:99533729-99533730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99528371..99530987-chr2:99533577..99536633,3	MCF-7	breast:
2	chr2:99532387..99535858-chr2:99543640..99546629,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10169003	0.84[EUR][1000 genomes]
rs10172158	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10181972	0.84[EUR][1000 genomes]
rs10192266	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11123755	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11887536	0.81[EUR][1000 genomes]
rs11893888	0.83[EUR][1000 genomes]
rs12468024	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12474283	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12712038	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12712041	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712042	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12712043	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13004700	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13004923	0.84[EUR][1000 genomes]
rs13005124	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13011428	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13025076	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13025913	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13028500	0.87[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1581250	0.84[EUR][1000 genomes]
rs1581251	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1607256	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17758170	0.92[CEU][hapmap]
rs1878585	0.84[EUR][1000 genomes]
rs1878589	0.92[CEU][hapmap]
rs1976766	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1983352	0.84[GIH][hapmap];0.80[TSI][hapmap]
rs2048949	0.83[AMR][1000 genomes]
rs4311103	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4850889	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4850890	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851167	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4851170	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4851171	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851173	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851174	0.86[CEU][hapmap];0.84[AMR][1000 genomes]
rs4851175	0.87[CEU][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4851176	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4851177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125264	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6419564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542841	0.88[CEU][hapmap]
rs6542845	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6714243	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6717372	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6724477	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6739176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742047	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6757098	0.88[CEU][hapmap]
rs6760065	0.88[CEU][hapmap]
rs7423519	0.92[CEU][hapmap]
rs7608889	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs883773	0.88[CEU][hapmap]
rs908672	0.92[ASW][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs925887	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs981602	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6542843	UNC50	cis	cerebellum	SCAN
rs6542843	LIPT1	cis	parietal	SCAN
rs6542843	LIPT1	cis	lymphoblastoid	seeQTL
rs6542843	TSGA10	cis	multi-tissue	Pritchard
rs6542843	FAHD2B	cis	parietal	SCAN
rs6542843	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6542843	TSGA10	cis	parietal	SCAN
rs6542843	LIPT1	cis	cerebellum	SCAN
rs6542843	TSGA10	cis	cerebellum	SCAN
rs6542843	TSGA10	cis	Lymphoblastoid	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99524400-99534400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:99526400-99534200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:99528000-99534000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:99528200-99534400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:99529200-99534000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:99529200-99534200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:99529400-99534000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:99530200-99534000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:99530400-99533800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:99530400-99534400	Enhancers	HMEC	breast
11	chr2:99531200-99534400	Enhancers	HSMM	muscle
12	chr2:99531200-99539000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:99531600-99534200	Enhancers	NHEK	skin
14	chr2:99532000-99534200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:99532000-99537400	Weak transcription	Gastric	stomach
16	chr2:99532200-99533800	Enhancers	A549	lung
17	chr2:99532200-99534000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:99532200-99534000	Enhancers	NHDF-Ad	bronchial
19	chr2:99532200-99534000	Enhancers	Osteobl	bone
20	chr2:99532200-99534200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:99532200-99534200	Enhancers	HSMMtube	muscle
22	chr2:99532400-99542800	Weak transcription	Pancreas	Pancrea
23	chr2:99532600-99533800	Enhancers	Fetal Muscle Leg	muscle
24	chr2:99532600-99534400	Enhancers	HUVEC	blood vessel
25	chr2:99533000-99534000	Enhancers	Brain Anterior Caudate	brain
26	chr2:99533400-99533800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:99533400-99533800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:99533400-99534000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:99533400-99534000	Enhancers	Fetal Brain Female	brain
30	chr2:99533400-99534200	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:99533600-99533800	Enhancers	NH-A	brain
32	chr2:99533600-99534400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:99533600-99536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:99533600-99536800	Weak transcription	Esophagus	oesophagus

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