Variant report

Variant	rs12324187
Chromosome Location	chr15:99750506-99750507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12324825	0.81[CEU][hapmap]
rs12591477	0.81[CEU][hapmap]
rs1377267	0.89[CEU][hapmap]
rs1530920	0.81[CEU][hapmap]
rs2623184	0.83[CHD][hapmap]
rs28377529	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28560310	0.89[EUR][1000 genomes]
rs3803472	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs62025687	0.92[EUR][1000 genomes]
rs7174431	1.00[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs735823	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8023421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8023490	0.87[CEU][hapmap]
rs8026991	0.85[CEU][hapmap]
rs8031175	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8032154	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs8038002	0.83[CHB][hapmap]
rs8038392	0.83[CEU][hapmap]
rs9672800	0.88[CEU][hapmap]

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	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	esv2760374	chr15:99739048-99754071	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12324187	TTC23	cis	cerebellum	SCAN
rs12324187	NR2F2	cis	parietal	SCAN
rs12324187	SYNM	cis	parietal	SCAN
rs12324187	TTC23	cis	multi-tissue	Pritchard
rs12324187	SYNM	cis	cerebellum	SCAN
rs12324187	TTC23	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99697000-99756400	Weak transcription	Stomach Mucosa	stomach
3	chr15:99717400-99761000	Weak transcription	Gastric	stomach
4	chr15:99717800-99758000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:99721200-99758400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:99722000-99758400	Weak transcription	Right Ventricle	heart
7	chr15:99722400-99752200	Weak transcription	Osteobl	bone
8	chr15:99722600-99757600	Weak transcription	Psoas Muscle	Psoas
9	chr15:99724400-99769600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:99726600-99758200	Weak transcription	HMEC	breast
11	chr15:99728400-99760000	Weak transcription	NHDF-Ad	bronchial
12	chr15:99732800-99758000	Weak transcription	Spleen	Spleen
13	chr15:99732800-99761000	Weak transcription	Lung	lung
14	chr15:99733000-99758400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:99733000-99760400	Weak transcription	Esophagus	oesophagus
16	chr15:99733200-99751800	Weak transcription	A549	lung
17	chr15:99733200-99756800	Weak transcription	Aorta	Aorta
18	chr15:99733200-99758200	Weak transcription	Colonic Mucosa	Colon
19	chr15:99733400-99752800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:99733400-99787400	Weak transcription	NHEK	skin
21	chr15:99734200-99752000	Weak transcription	Fetal Heart	heart
22	chr15:99734200-99758200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:99734400-99758000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:99734600-99757800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:99735200-99758200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:99737200-99752200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:99737200-99752600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:99737200-99755200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:99737200-99758000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:99737400-99758000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:99739400-99752400	Weak transcription	NH-A	brain
32	chr15:99739400-99759200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:99739800-99757600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:99740000-99758400	Weak transcription	Hela-S3	cervix
35	chr15:99740200-99752000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:99740200-99752200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:99740200-99752200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:99740200-99752400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:99740200-99752600	Weak transcription	NHLF	lung
40	chr15:99740200-99754800	Weak transcription	Adipose Nuclei	Adipose
41	chr15:99740200-99754800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:99740200-99755400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:99740200-99755400	Weak transcription	HSMM	muscle
44	chr15:99740200-99756800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:99740200-99757000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:99740200-99757600	Weak transcription	Dnd41	blood
47	chr15:99740200-99758000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:99740200-99758000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr15:99740200-99758000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:99740200-99758000	Weak transcription	HSMMtube	muscle

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