Variant report

Variant	rs9371541
Chromosome Location	chr6:150212869-150212870
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr6:150212432-150212900	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
2	chr6:150212160..150213980-chr6:150214968..150218117,3	K562	blood:

Variant related genes	Relation type
RAET1E	TF binding region
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000164520	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1334510	0.82[ASN][1000 genomes]
rs2342767	0.91[ASN][1000 genomes]
rs2342769	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2342770	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3823021	0.94[ASN][1000 genomes]
rs4869763	0.94[ASN][1000 genomes]
rs4869764	0.94[ASN][1000 genomes]
rs6557133	0.82[ASN][1000 genomes]
rs6933882	0.94[ASN][1000 genomes]
rs6935829	0.88[AFR][1000 genomes]
rs6939761	0.94[ASN][1000 genomes]
rs7740145	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7742692	0.94[ASN][1000 genomes]
rs7742993	0.91[ASN][1000 genomes]
rs7744821	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7747457	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7753544	0.91[ASN][1000 genomes]
rs7756850	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7757972	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7757984	0.91[ASN][1000 genomes]
rs7758020	0.91[ASN][1000 genomes]
rs7758033	0.91[ASN][1000 genomes]
rs7763849	0.91[ASN][1000 genomes]
rs7764376	0.94[ASN][1000 genomes]
rs7767588	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7767592	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7768626	0.91[ASN][1000 genomes]
rs7768665	0.91[ASN][1000 genomes]
rs7769118	0.91[ASN][1000 genomes]
rs7774787	0.91[ASN][1000 genomes]
rs9322228	0.91[ASN][1000 genomes]
rs9371215	0.82[ASN][1000 genomes]
rs9371223	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9371533	0.89[ASN][1000 genomes]
rs9371542	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9371544	0.88[AFR][1000 genomes]
rs9383577	0.91[ASN][1000 genomes]
rs9383584	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9383912	0.91[ASN][1000 genomes]
rs9383913	0.91[ASN][1000 genomes]
rs9383914	0.91[ASN][1000 genomes]
rs9383921	0.94[ASN][1000 genomes]
rs9397058	0.91[ASN][1000 genomes]
rs9397398	0.82[ASN][1000 genomes]
rs9397420	0.91[ASN][1000 genomes]
rs9397434	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9968871	0.91[ASN][1000 genomes]
rs9969044	0.91[ASN][1000 genomes]

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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9371541	NUP43	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150205600-150216000	Weak transcription	Right Atrium	heart
2	chr6:150205800-150216000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:150206000-150216000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:150209600-150215800	Weak transcription	Adipose Nuclei	Adipose
5	chr6:150209600-150216000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:150209600-150222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:150212000-150213200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:150212000-150216000	Weak transcription	Placenta	Placenta
9	chr6:150212000-150216000	Weak transcription	Lung	lung
10	chr6:150212000-150216000	Weak transcription	Ovary	ovary
11	chr6:150212000-150216000	Weak transcription	Psoas Muscle	Psoas
12	chr6:150212000-150216200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:150212200-150213200	Enhancers	HMEC	breast
14	chr6:150212200-150215800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:150212200-150215800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:150212400-150216200	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:150212600-150215800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:150212600-150216000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:150212600-150216000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:150212600-150216000	Weak transcription	Esophagus	oesophagus
21	chr6:150212600-150216200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:150212600-150216200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:150212600-150216200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:150212600-150216200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:150212600-150216400	Weak transcription	HSMMtube	muscle
26	chr6:150212800-150215800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:150212800-150215800	Weak transcription	A549	lung
28	chr6:150212800-150215800	Weak transcription	Hela-S3	cervix
29	chr6:150212800-150215800	Weak transcription	NHDF-Ad	bronchial
30	chr6:150212800-150215800	Weak transcription	NHEK	skin
31	chr6:150212800-150216000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:150212800-150216200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:150212800-150216200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:150212800-150216400	Weak transcription	Osteobl	bone
35	chr6:150212800-150216600	Weak transcription	HSMM	muscle

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