Variant report

Variant	rs10864029
Chromosome Location	chr1:213078943-213078944
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10864023	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10864028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11120044	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11120062	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120067	0.83[AMR][1000 genomes]
rs11576299	0.80[AMR][1000 genomes]
rs11576311	0.81[AMR][1000 genomes]
rs11582817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11586314	0.85[AMR][1000 genomes]
rs11586464	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12036853	0.92[ASN][1000 genomes]
rs12136547	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12140722	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12140754	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12184323	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12404754	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12405293	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12567976	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12754609	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12755947	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1284852	0.97[ASN][1000 genomes]
rs1284854	0.97[ASN][1000 genomes]
rs1284855	0.83[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs1284856	0.90[ASN][1000 genomes]
rs1587175	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2201601	0.90[EUR][1000 genomes]
rs2359325	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3207090	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816952	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3816953	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3816957	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4951471	0.97[ASN][1000 genomes]
rs4951474	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4951655	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6656128	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6656232	0.84[AMR][1000 genomes]
rs6670064	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6679848	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6679938	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6679951	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6702876	0.92[ASN][1000 genomes]
rs7523310	0.82[AMR][1000 genomes]
rs7523329	0.82[AMR][1000 genomes]
rs7533476	0.82[AMR][1000 genomes]
rs7533575	0.82[AMR][1000 genomes]
rs7541559	0.89[ASN][1000 genomes]
rs870547	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs871767	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1007129	chr1:213037244-213083261	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs10864029	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs10864029	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs10864029	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs10864029	FLVCR1-AS1	cis	lung	GTEx
rs10864029	FLVCR1-AS1	cis	Muscle Skeletal	GTEx
rs10864029	FLVCR1-AS1	cis	Whole Blood	GTEx
rs10864029	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs10864029	LQK1	cis	normal skin	skin_eQTL
rs10864029	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs10864029	VASH2	Cis_1M	lymphoblastoid	RTeQTL
rs10864029	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs10864029	FLVCR1-AS1	cis	Stomach	GTEx
rs10864029	LQK1	cis	uninvolved skin	skin_eQTL
rs10864029	FLVCR1	cis	multi-tissue	Pritchard
rs10864029	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs10864029	LQK1	cis	lesional skin	skin_eQTL
rs10864029	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs10864029	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs10864029	FLVCR1-AS1	cis	Thyroid	GTEx
rs10864029	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213073200-213079200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr1:213073200-213079400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
3	chr1:213073200-213079800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr1:213073600-213079200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr1:213073800-213079200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:213073800-213079200	Weak transcription	Right Atrium	heart
7	chr1:213073800-213089000	Weak transcription	Pancreas	Pancrea
8	chr1:213075200-213079000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
9	chr1:213076800-213079200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:213076800-213083600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:213078000-213080000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
12	chr1:213078600-213079400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
13	chr1:213078600-213079800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:213078800-213079600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell

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