Variant report

Variant	rs62482252
Chromosome Location	chr7:100274063-100274064
allele	A/C
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	POLR2A	chr7:100270661-100278926	K562	blood:	n/a	n/a
2	GABPA	chr7:100273283-100274126	SK-N-SH	brain:	n/a	chr7:100273494-100273503
3	ELF1	chr7:100273153-100274233	GM12878	blood:	n/a	chr7:100273761-100273773 chr7:100273566-100273579
4	GABPA	chr7:100273169-100274076	MCF-7	breast:	n/a	chr7:100273494-100273503
5	MXI1	chr7:100270587-100274930	SK-N-SH	brain:	n/a	chr7:100273223-100273238 chr7:100273221-100273236 chr7:100271103-100271112 chr7:100273287-100273302 chr7:100273289-100273304
6	MAZ	chr7:100270689-100274069	IMR90	lung:	n/a	chr7:100271101-100271110 chr7:100271097-100271116 chr7:100271102-100271111 chr7:100271100-100271113 chr7:100271102-100271111 chr7:100273223-100273232 chr7:100271100-100271113 chr7:100271101-100271112 chr7:100272135-100272145
7	JUND	chr7:100270590-100276358	SK-N-SH	brain:	n/a	chr7:100273500-100273509 chr7:100271366-100271375 chr7:100273496-100273505 chr7:100271086-100271095 chr7:100273495-100273504 chr7:100273499-100273508 chr7:100273959-100273968 chr7:100273775-100273784 chr7:100273598-100273607 chr7:100271858-100271867 chr7:100272130-100272139
8	POLR2A	chr7:100273966-100279009	GM12878	blood:	n/a	n/a
9	ELF1	chr7:100273198-100274216	MCF-7	breast:	n/a	chr7:100273761-100273773 chr7:100273566-100273579
10	POLR2A	chr7:100273065-100274696	MCF-7	breast:	n/a	n/a
11	MXI1	chr7:100273166-100274648	IMR90	lung:	n/a	chr7:100273223-100273238 chr7:100273221-100273236 chr7:100273287-100273302 chr7:100273289-100273304
12	POLR2A	chr7:100273937-100274135	K562	blood:	n/a	n/a
13	POLR2A	chr7:100272997-100278980	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100179385..100182357-chr7:100273234..100275046,2	K562	blood:
2	chr7:100235870..100241765-chr7:100269603..100274523,10	K562	blood:
3	chr7:100201513..100203837-chr7:100271300..100274333,3	K562	blood:
4	chr7:100201777..100204545-chr7:100274032..100275597,2	MCF-7	breast:
5	chr7:100199137..100204002-chr7:100270035..100274228,6	MCF-7	breast:
6	chr7:100024810..100029555-chr7:100269638..100276218,15	K562	blood:
7	chr7:100243852..100245998-chr7:100273803..100276710,3	MCF-7	breast:
8	chr7:100178369..100186125-chr7:100269651..100278553,26	MCF-7	breast:
9	chr7:100024969..100026513-chr7:100273974..100276218,2	MCF-7	breast:
10	chr7:100201513..100203837-chr7:100271300..100274333,4	K562	blood:
11	chr7:100273325..100275099-chr7:100303615..100305152,2	K562	blood:
12	chr7:100234354..100241214-chr7:100269812..100274154,10	K562	blood:
13	chr7:100024682..100026645-chr7:100273094..100274953,2	K562	blood:
14	chr7:100273516..100275099-chr7:100303471..100305152,2	K562	blood:
15	chr7:100063964..100066067-chr7:100271416..100274399,2	K562	blood:
16	chr7:100208069..100211610-chr7:100269776..100275197,5	K562	blood:
17	chr7:100179326..100185857-chr7:100269460..100275597,19	MCF-7	breast:
18	chr7:100222858..100232262-chr7:100269297..100275934,19	MCF-7	breast:

Variant related genes	Relation type
GNB2	TF binding region
ENSG00000166925	Chromatin interaction
ENSG00000077080	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000106336	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10953300	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953301	0.97[ASN][1000 genomes]
rs11520986	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760602	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11765509	0.88[EUR][1000 genomes]
rs11769012	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11772052	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11772705	0.84[ASN][1000 genomes]
rs11772849	0.90[EUR][1000 genomes]
rs11973874	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11974395	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979818	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11980509	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11983334	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11984421	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12531792	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272572	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4727459	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729602	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4729605	0.88[EUR][1000 genomes]
rs4729606	0.88[EUR][1000 genomes]
rs4729607	0.86[EUR][1000 genomes]
rs62482249	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482250	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482251	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62483567	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62483569	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62483570	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription 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
10	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv888793	chr7:100266081-100279163	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv888794	chr7:100266081-100283261	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv888795	chr7:100266081-100298626	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62482252	PERQ1	Cis_1M	lymphoblastoid	RTeQTL
rs62482252	MOSPD3	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100270600-100274200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr7:100270600-100274200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:100270600-100274200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:100270600-100274200	Active TSS	Colonic Mucosa	Colon
5	chr7:100270600-100274200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr7:100270600-100274200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr7:100270600-100274200	Active TSS	Psoas Muscle	Psoas
8	chr7:100270600-100274200	Active TSS	Right Atrium	heart
9	chr7:100270600-100274200	Active TSS	Right Ventricle	heart
10	chr7:100270600-100274400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr7:100270600-100274400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr7:100270600-100274400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr7:100270600-100274400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr7:100270600-100274400	Active TSS	Brain Anterior Caudate	brain
15	chr7:100270600-100274400	Active TSS	HSMM	muscle
16	chr7:100270800-100274200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:100270800-100274200	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr7:100270800-100274200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:100270800-100274200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:100270800-100274200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:100270800-100274200	Active TSS	Muscle Satellite Cultured Cells	--
22	chr7:100270800-100274200	Active TSS	Ovary	ovary
23	chr7:100270800-100274200	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr7:100270800-100274200	Active TSS	HSMMtube	muscle
25	chr7:100270800-100274200	Active TSS	NHDF-Ad	bronchial
26	chr7:100270800-100274200	Active TSS	NHLF	lung
27	chr7:100270800-100274200	Active TSS	Osteobl	bone
28	chr7:100271000-100274200	Active TSS	Small Intestine	intestine
29	chr7:100271000-100274200	Active TSS	NH-A	brain
30	chr7:100271400-100274200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr7:100272400-100274200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:100272800-100277400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr7:100273000-100274200	Active TSS	Primary B cells from cord blood	blood
34	chr7:100273200-100274600	Transcr. at gene 5' and 3'	Dnd41	blood
35	chr7:100273200-100277400	Enhancers	Fetal Heart	heart
36	chr7:100273400-100274200	Weak transcription	A549	lung
37	chr7:100273400-100274200	Weak transcription	HepG2	liver
38	chr7:100273400-100274400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr7:100273600-100274200	Active TSS	Primary hematopoietic stem cells	blood
40	chr7:100273600-100274200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr7:100273600-100274200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr7:100273600-100274600	Enhancers	Fetal Brain Male	brain
43	chr7:100273600-100277800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr7:100273800-100274200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr7:100273800-100274200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr7:100273800-100274200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:100273800-100274200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:100273800-100274200	Weak transcription	Brain Substantia Nigra	brain
49	chr7:100273800-100274200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
50	chr7:100273800-100274200	Weak transcription	Placenta Amnion	Placenta Amnion

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