Variant report

Variant	rs10230054
Chromosome Location	chr7:19960020-19960021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MACC1-1	chr7:19959489-19960253	NONHSAT119395

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10226448	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10226787	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10229052	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10233274	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10242012	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10243275	0.82[AMR][1000 genomes]
rs10243855	0.80[EUR][1000 genomes]
rs10245082	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10245287	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10248922	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10249779	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10250128	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10258669	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10261330	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10265569	0.83[AMR][1000 genomes]
rs10266457	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10271196	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10272491	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10276105	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10277995	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12530927	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12539212	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12672377	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12672567	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13228331	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13228500	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13228531	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13239768	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13241328	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13307910	0.89[JPT][hapmap]
rs17142178	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2214319	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2214320	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2390203	0.80[EUR][1000 genomes]
rs28852390	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2892957	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34292170	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34359626	0.80[EUR][1000 genomes]
rs36157620	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36200915	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4994101	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4994102	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs58159256	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6461466	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6946403	0.95[JPT][hapmap]
rs6977047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977654	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73267155	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7779502	0.88[AMR][1000 genomes]
rs7780131	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7789051	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7796408	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7796434	0.87[AMR][1000 genomes]
rs879661	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs879662	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9654951	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9654952	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9654953	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9655183	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9655184	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9655185	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9655186	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes]

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	nsv1018601	chr7:19272360-20008881	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1033223	chr7:19682192-20461375	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv538795	chr7:19682192-20461375	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	esv1847477	chr7:19778086-19970584	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv887826	chr7:19816240-20033899	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1844137	chr7:19862221-19970584	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
7	nsv1027445	chr7:19947297-20211733	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19954800-19973000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:19956200-19960200	Weak transcription	NH-A	brain
3	chr7:19956400-19988000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:19958400-19960400	Enhancers	NHEK	skin
5	chr7:19958600-19960800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:19958600-19961200	Enhancers	Fetal Lung	lung
7	chr7:19959000-19960400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:19959000-19960800	Enhancers	HUVEC	blood vessel
9	chr7:19959200-19960200	Enhancers	Colon Smooth Muscle	Colon
10	chr7:19959400-19960400	Enhancers	Fetal Muscle Leg	muscle
11	chr7:19959400-19960400	Enhancers	HSMM	muscle
12	chr7:19959400-19960600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:19959400-19960800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:19959400-19960800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr7:19959600-19960400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr7:19959600-19960400	Enhancers	Stomach Smooth Muscle	stomach
17	chr7:19959600-19961200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr7:19959800-19960400	Enhancers	Ovary	ovary
19	chr7:19959800-19960600	Enhancers	NHLF	lung
20	chr7:19959800-19960800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:19960000-19960600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr7:19960000-19960800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr7:19960000-19960800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:19960000-19983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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