Variant report

Variant	rs12907394
Chromosome Location	chr15:99770137-99770138
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99768986..99771522-chr15:99790162..99791793,2	K562	blood:

Variant related genes	Relation type
ENSG00000168904	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10152912	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1223950	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1223951	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1238348	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12437806	0.97[ASN][1000 genomes]
rs12911768	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915819	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1567416	0.83[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1976589	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1976590	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2048301	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602016	1.00[ASW][hapmap]
rs2602018	0.82[CHD][hapmap]
rs2602026	0.82[CHD][hapmap]
rs2602030	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2602036	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs2862139	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3210942	1.00[ASW][hapmap]
rs3937681	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4344722	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4965217	0.86[ASW][hapmap];0.82[CHD][hapmap]
rs4965224	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6598231	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164003	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7183226	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs8042021	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920418	0.83[CEU][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS 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 miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS 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	30 gene(s)	inside rSNPs	diseases
11	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
12	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
13	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
16	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers 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	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12907394	NR2F2	cis	parietal	SCAN
rs12907394	TTC23	cis	parietal	SCAN
rs12907394	TTC23	cis	multi-tissue	Pritchard
rs12907394	SYNM	cis	cerebellum	SCAN
rs12907394	NR2F2	cis	cerebellum	SCAN
rs12907394	TTC23	cis	cerebellum	SCAN
rs12907394	ADAMTS17	cis	parietal	SCAN
rs12907394	TTC23	cis	lymphoblastoid	seeQTL
rs12907394	SYNM	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99733400-99787400	Weak transcription	NHEK	skin
3	chr15:99749800-99789400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:99750000-99789400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:99756600-99789400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:99758600-99789400	Weak transcription	Brain Substantia Nigra	brain
7	chr15:99759200-99788400	Weak transcription	Fetal Thymus	thymus
8	chr15:99759400-99781800	Weak transcription	Spleen	Spleen
9	chr15:99759400-99788600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:99759400-99788600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:99761000-99778400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:99761400-99771000	Weak transcription	GM12878-XiMat	blood
13	chr15:99761400-99781800	Weak transcription	Pancreas	Pancrea
14	chr15:99761400-99788400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:99761800-99772800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:99762000-99780400	Weak transcription	Esophagus	oesophagus
17	chr15:99762400-99772800	Weak transcription	A549	lung
18	chr15:99762600-99789400	Weak transcription	Gastric	stomach
19	chr15:99762800-99774800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:99765400-99784000	Weak transcription	Hela-S3	cervix
21	chr15:99765600-99789400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:99765800-99778600	Weak transcription	Psoas Muscle	Psoas
23	chr15:99765800-99778800	Weak transcription	HUVEC	blood vessel
24	chr15:99765800-99789400	Weak transcription	Lung	lung
25	chr15:99766200-99770200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr15:99766200-99780000	Weak transcription	Placenta	Placenta
27	chr15:99767000-99778600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:99767200-99781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:99768000-99778200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr15:99768200-99788600	Weak transcription	Colonic Mucosa	Colon
31	chr15:99768200-99789200	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:99768400-99776400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:99768600-99774800	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:99768600-99775000	Weak transcription	Fetal Stomach	stomach
35	chr15:99768600-99776000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:99768600-99778600	Weak transcription	Aorta	Aorta
37	chr15:99768600-99780000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:99768600-99780600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:99768600-99780800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr15:99768600-99781000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:99768600-99781000	Weak transcription	Right Ventricle	heart
42	chr15:99768600-99787200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:99768600-99787200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:99768600-99787200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:99768600-99787200	Weak transcription	HepG2	liver
46	chr15:99768600-99788400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:99768600-99788400	Weak transcription	Ovary	ovary
48	chr15:99768800-99772600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:99768800-99772800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr15:99768800-99772800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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