Variant report

Variant	rs7540071
Chromosome Location	chr1:241646582-241646583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241646443..241651437-chr1:241651445..241654937,7	K562	blood:
2	chr1:241644657..241646785-chr1:241661532..241663893,2	K562	blood:
3	chr1:241642545..241644863-chr1:241645062..241646995,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10802967	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926503	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10926511	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059375	0.94[AFR][1000 genomes]
rs12059383	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12062672	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065955	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12072983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2105079	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2341939	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765801	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4660098	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660102	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57644653	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[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	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh 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	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7540071	NR2F6	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241639000-241657000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:241639600-241646800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:241643800-241657800	Weak transcription	Psoas Muscle	Psoas
4	chr1:241644200-241649800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:241644400-241646600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:241644400-241646600	Enhancers	NHDF-Ad	bronchial
7	chr1:241644600-241646600	Enhancers	HUVEC	blood vessel
8	chr1:241644600-241649600	Enhancers	NHLF	lung
9	chr1:241644600-241657200	Weak transcription	Right Ventricle	heart
10	chr1:241644800-241647000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:241644800-241647600	Enhancers	HSMM	muscle
12	chr1:241645200-241647000	Enhancers	HMEC	breast
13	chr1:241645200-241647600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:241645400-241646600	Enhancers	HSMMtube	muscle
15	chr1:241645400-241647000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:241645400-241647000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:241645800-241647000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:241645800-241647000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:241645800-241647000	Enhancers	A549	lung
20	chr1:241645800-241647000	Enhancers	NH-A	brain
21	chr1:241645800-241647000	Enhancers	NHEK	skin
22	chr1:241646000-241646800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:241646000-241646800	Enhancers	K562	blood
24	chr1:241646400-241646600	Flanking Active TSS	Osteobl	bone
25	chr1:241646400-241646800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:241646400-241646800	Weak transcription	Hela-S3	cervix
27	chr1:241646400-241657200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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