Variant report

Variant	rs72722847
Chromosome Location	chr15:31682346-31682347
allele	C/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	CTCF	chr15:31682320-31682470	HMF	breast:	n/a	n/a
2	CTCF	chr15:31682300-31682450	HepG2	liver:	n/a	n/a
3	CTCF	chr15:31682280-31682430	Hela-S3	cervix:	n/a	n/a
4	KAP1	chr15:31682287-31682923	HEK293	kidney:	n/a	n/a
5	RAD21	chr15:31682288-31682551	H1-hESC	embryonic stem cell:	n/a	n/a
6	SETDB1	chr15:31682289-31682884	U2OS	brain:	n/a	n/a
7	CTCF	chr15:31682300-31682450	HPAF	blood vessel:	n/a	n/a
8	SMC3	chr15:31682273-31682402	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr15:31682335-31682468	HepG2	liver:	n/a	n/a
10	CTCF	chr15:31682300-31682450	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31682078..31683956-chr15:31730554..31733122,2	K562	blood:

Variant related genes	Relation type
KLF13	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1075232	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12437749	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12437800	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438813	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12439239	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12439853	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16956707	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16956738	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34959140	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4450360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56396205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58156651	0.87[AMR][1000 genomes]
rs66581165	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67634762	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72722829	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72722861	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72724938	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9672214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9672538	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer 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 target site	42 gene(s)	inside rSNPs	diseases
6	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv903841	chr15:31616674-31697242	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv903842	chr15:31621321-31697242	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv456748	chr15:31621321-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv568801	chr15:31621321-31697642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1810782	chr15:31633161-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv903843	chr15:31672947-31723279	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv3423388	chr15:31682185-31685233	Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs72722847	CTD-3092A11.2	cis	Whole Blood	GTEx
rs72722847	CHRNA7	cis	Artery Tibial	GTEx
rs72722847	CHRNA7	cis	Thyroid	GTEx
rs72722847	RP11-932O9.7	cis	lung	GTEx
rs72722847	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs72722847	CHRNA7	cis	Whole Blood	GTEx
rs72722847	RP11-932O9.7	cis	Artery Tibial	GTEx
rs72722847	GOLGA8R	cis	Heart Left Ventricle	GTEx
rs72722847	CTD-3092A11.2	cis	lung	GTEx
rs72722847	CTD-3092A11.2	cis	Artery Tibial	GTEx
rs72722847	GOLGA8R	cis	Artery Tibial	GTEx
rs72722847	CHRNA7	cis	lung	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31670800-31683800	Weak transcription	Small Intestine	intestine
2	chr15:31673600-31684000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:31674200-31684000	Weak transcription	Colonic Mucosa	Colon
4	chr15:31674600-31683800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:31674600-31684000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:31675000-31684000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:31675200-31684000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:31675800-31683800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:31675800-31683800	Weak transcription	Right Atrium	heart
10	chr15:31675800-31684000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:31676600-31683000	Weak transcription	Fetal Intestine Large	intestine
12	chr15:31677000-31683400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr15:31677000-31684000	Weak transcription	Gastric	stomach
14	chr15:31680200-31683600	Weak transcription	Right Ventricle	heart
15	chr15:31680400-31682800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:31680400-31683000	Weak transcription	Lung	lung
17	chr15:31680400-31683600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:31680400-31683800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:31680400-31683800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:31680400-31684000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:31680400-31684000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:31680400-31684000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr15:31680400-31684000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:31680400-31684000	Weak transcription	Brain Anterior Caudate	brain
25	chr15:31680400-31684000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:31680400-31684000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:31680400-31684000	Weak transcription	Brain Substantia Nigra	brain
28	chr15:31680400-31684000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:31680400-31684000	Weak transcription	Esophagus	oesophagus
30	chr15:31680400-31684200	Weak transcription	Spleen	Spleen
31	chr15:31680600-31683800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:31680600-31684000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:31680600-31684000	Weak transcription	Liver	Liver
34	chr15:31680600-31684000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:31680600-31684000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:31680600-31684000	Weak transcription	GM12878-XiMat	blood
37	chr15:31680600-31684000	Weak transcription	Hela-S3	cervix
38	chr15:31680800-31682800	Weak transcription	Fetal Heart	heart
39	chr15:31680800-31684000	Weak transcription	Primary T cells from cord blood	blood
40	chr15:31680800-31684000	Weak transcription	Pancreas	Pancrea
41	chr15:31680800-31684000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:31680800-31684000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:31680800-31684000	Weak transcription	HMEC	breast
44	chr15:31680800-31684000	Weak transcription	Osteobl	bone
45	chr15:31680800-31684200	Weak transcription	Dnd41	blood
46	chr15:31681200-31682600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:31681200-31684000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:31681400-31683200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr15:31681400-31683200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr15:31681400-31683400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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