Variant report

Variant	rs12438318
Chromosome Location	chr15:31680445-31680446
allele	A/G
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	MAX	chr15:31680004-31680498	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr15:31679771-31680464	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr15:31679494-31680646	SK-N-SH	brain:	n/a	chr15:31680518-31680532

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31673644..31676164-chr15:31678034..31680929,2	K562	blood:

Variant related genes	Relation type
KLF13	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10438322	0.87[CHD][hapmap];0.85[JPT][hapmap]
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]
rs12437996	0.85[JPT][hapmap]
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]
rs1370062	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs16956707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16956738	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1972825	0.85[JPT][hapmap]
rs34959140	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743235	0.81[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
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]
rs6493531	0.85[JPT][hapmap]
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]
rs72722847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:13 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12438318	CHRNA7	cis	Thyroid	GTEx
rs12438318	RP11-932O9.7	cis	Artery Tibial	GTEx
rs12438318	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs12438318	CHRNA7	cis	Whole Blood	GTEx
rs12438318	CTD-3092A11.2	cis	lung	GTEx
rs12438318	CTD-3092A11.2	cis	Artery Tibial	GTEx
rs12438318	CTD-3092A11.2	cis	Whole Blood	GTEx
rs12438318	RP11-932O9.7	cis	lung	GTEx
rs12438318	GOLGA8R	cis	Heart Left Ventricle	GTEx
rs12438318	CHRNA7	cis	Artery Tibial	GTEx
rs12438318	CHRNA7	cis	lung	GTEx

Chromatin state (count:82 , 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	chr15:31675200-31681600	Weak transcription	Fetal Stomach	stomach
8	chr15:31675200-31684000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:31675800-31683800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:31675800-31683800	Weak transcription	Right Atrium	heart
11	chr15:31675800-31684000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:31676600-31683000	Weak transcription	Fetal Intestine Large	intestine
13	chr15:31676800-31681000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:31676800-31681000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr15:31677000-31681000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr15:31677000-31683400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr15:31677000-31684000	Weak transcription	Gastric	stomach
18	chr15:31677200-31680800	Enhancers	Primary T cells from cord blood	blood
19	chr15:31677200-31681200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:31677200-31681600	Weak transcription	Primary B cells from cord blood	blood
21	chr15:31677400-31681800	Weak transcription	Left Ventricle	heart
22	chr15:31677600-31681200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr15:31677800-31680600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr15:31677800-31680600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:31678600-31680800	Enhancers	Dnd41	blood
26	chr15:31678800-31680800	Enhancers	Fetal Heart	heart
27	chr15:31679200-31680600	Enhancers	Liver	Liver
28	chr15:31679200-31681400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:31679400-31680600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:31679400-31680600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:31679400-31680600	Enhancers	Fetal Brain Female	brain
32	chr15:31679400-31680600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr15:31679400-31680600	Enhancers	HSMM	muscle
34	chr15:31679400-31680600	Enhancers	NH-A	brain
35	chr15:31679400-31680600	Enhancers	NHEK	skin
36	chr15:31679400-31680800	Enhancers	Pancreas	Pancrea
37	chr15:31679400-31680800	Enhancers	Stomach Mucosa	stomach
38	chr15:31679400-31680800	Enhancers	HMEC	breast
39	chr15:31679400-31681400	Enhancers	NHDF-Ad	bronchial
40	chr15:31679400-31682200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr15:31679800-31680600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:31679800-31680600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:31679800-31680600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:31679800-31680600	Enhancers	Fetal Muscle Leg	muscle
45	chr15:31679800-31680600	Enhancers	Rectal Smooth Muscle	rectum
46	chr15:31679800-31680600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr15:31679800-31680600	Enhancers	GM12878-XiMat	blood
48	chr15:31679800-31680600	Enhancers	Hela-S3	cervix
49	chr15:31679800-31680600	Enhancers	NHLF	lung
50	chr15:31679800-31680800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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