Variant report

Variant	rs7562080
Chromosome Location	chr2:64357206-64357207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64356583..64359490-chr2:64359820..64361571,2	K562	blood:
2	chr2:64355620..64357775-chr2:64369401..64371432,2	K562	blood:
3	chr2:64352794..64354467-chr2:64356091..64358987,2	K562	blood:

Variant related genes	Relation type
ENSG00000225889	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2581047	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs329499	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs329500	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6726519	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7581647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604693	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7562080	PELI1	cis	parietal	SCAN
rs7562080	AIRE	trans	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64323600-64364400	Weak transcription	Fetal Brain Male	brain
2	chr2:64335000-64365200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:64340400-64370200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:64342000-64365200	Weak transcription	Left Ventricle	heart
5	chr2:64342200-64358600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:64342800-64360600	Weak transcription	K562	blood
7	chr2:64342800-64362200	Weak transcription	Thymus	Thymus
8	chr2:64343800-64361800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:64344000-64361000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:64344400-64360600	Weak transcription	HUVEC	blood vessel
11	chr2:64344400-64361000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:64347400-64368800	Weak transcription	Spleen	Spleen
13	chr2:64347800-64358000	Weak transcription	Fetal Heart	heart
14	chr2:64348400-64364600	Weak transcription	Adipose Nuclei	Adipose
15	chr2:64348400-64366400	Weak transcription	Right Atrium	heart
16	chr2:64348600-64359000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:64348600-64359200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:64348600-64359400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:64348600-64361600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:64348600-64365200	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:64349000-64359400	Weak transcription	Fetal Thymus	thymus
22	chr2:64349800-64363800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:64350400-64364600	Weak transcription	Primary B cells from cord blood	blood
24	chr2:64350600-64359400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:64351200-64359800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:64351400-64364400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:64353200-64358200	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:64353600-64357800	Enhancers	HepG2	liver
29	chr2:64354200-64358800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr2:64354600-64365200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:64354800-64363600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr2:64354800-64364200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr2:64355000-64357600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr2:64355000-64357800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr2:64355000-64357800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:64355000-64357800	Enhancers	Brain Anterior Caudate	brain
37	chr2:64355000-64357800	Enhancers	Brain Substantia Nigra	brain
38	chr2:64355000-64359400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:64355000-64360600	Enhancers	Brain Hippocampus Middle	brain
40	chr2:64355000-64362400	Weak transcription	Small Intestine	intestine
41	chr2:64355400-64368800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:64355600-64357800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:64355800-64357800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:64355800-64357800	Enhancers	Colon Smooth Muscle	Colon
45	chr2:64355800-64358400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:64355800-64364400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:64356000-64357800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:64356000-64358400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr2:64356200-64357800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:64356200-64358200	Enhancers	Rectal Mucosa Donor 31	rectum

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