Variant report

Variant	rs12913324
Chromosome Location	chr15:42768379-42768380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42766882..42770681-chr15:42773569..42778929,5	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10454039	0.82[EUR][1000 genomes]
rs1060291	0.81[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1062038	0.89[YRI][hapmap]
rs10851410	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs10851411	0.90[CEU][hapmap];0.90[TSI][hapmap]
rs11022	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11070374	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs11636577	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs11638208	0.96[EUR][1000 genomes]
rs12101559	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs12324113	0.85[EUR][1000 genomes]
rs12324717	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs12443246	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898937	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903432	0.87[EUR][1000 genomes]
rs12906697	0.82[EUR][1000 genomes]
rs16973265	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1900920	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900921	0.86[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs2241998	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs2255995	0.86[EUR][1000 genomes]
rs2412715	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2595939	0.87[EUR][1000 genomes]
rs2595940	0.90[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2595941	0.85[EUR][1000 genomes]
rs2617235	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617236	0.90[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs2617237	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617238	0.80[ASN][1000 genomes]
rs28886308	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899051	0.86[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2899057	0.83[EUR][1000 genomes]
rs3742997	0.84[AFR][1000 genomes]
rs3986280	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs4573906	0.87[EUR][1000 genomes]
rs4923948	0.86[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs4924678	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924684	0.82[EUR][1000 genomes]
rs56357092	0.82[EUR][1000 genomes]
rs57502147	0.81[AFR][1000 genomes]
rs62022317	0.87[EUR][1000 genomes]
rs7169615	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023929	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8033412	0.86[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs8034232	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8034238	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036544	0.95[ASN][1000 genomes]
rs9302112	0.90[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12913324	CXorf57	trans	parietal	SCAN
rs12913324	SNAP23	cis	parietal	SCAN
rs12913324	MAP1A	cis	parietal	SCAN
rs12913324	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42744200-42781800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:42744200-42782400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:42750000-42782600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:42750200-42782400	Weak transcription	Aorta	Aorta
5	chr15:42750800-42782400	Weak transcription	Ovary	ovary
6	chr15:42751000-42782400	Weak transcription	Fetal Lung	lung
7	chr15:42754600-42782400	Weak transcription	HSMMtube	muscle
8	chr15:42756000-42777600	Weak transcription	Lung	lung
9	chr15:42756000-42782600	Weak transcription	Esophagus	oesophagus
10	chr15:42756200-42782400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:42757800-42782600	Weak transcription	Gastric	stomach
12	chr15:42758000-42781600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:42758000-42782400	Weak transcription	NHLF	lung
14	chr15:42758200-42770600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:42758200-42770800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:42758200-42776200	Weak transcription	HepG2	liver
17	chr15:42758200-42781600	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:42758200-42781600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:42758200-42781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:42758400-42775400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:42758400-42775400	Weak transcription	Spleen	Spleen
22	chr15:42758400-42776800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:42758400-42780000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:42758400-42780400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:42758400-42780600	Weak transcription	NHEK	skin
26	chr15:42758400-42781800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr15:42758400-42781800	Weak transcription	Brain Anterior Caudate	brain
28	chr15:42758400-42782200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:42758400-42782200	Weak transcription	Fetal Brain Female	brain
30	chr15:42758400-42782200	Weak transcription	Thymus	Thymus
31	chr15:42759800-42782200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:42760200-42775000	Weak transcription	Primary B cells from cord blood	blood
33	chr15:42761400-42782000	Weak transcription	Fetal Stomach	stomach
34	chr15:42761600-42775000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:42761800-42782400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:42762400-42771000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:42762400-42775400	Weak transcription	Placenta	Placenta
38	chr15:42763400-42777200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr15:42763400-42777200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:42763400-42777400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:42763400-42782400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:42763600-42774400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:42763600-42775000	Weak transcription	Dnd41	blood
44	chr15:42763600-42780000	Weak transcription	Hela-S3	cervix
45	chr15:42763600-42780800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr15:42763600-42781600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:42763600-42782200	Weak transcription	HMEC	breast
48	chr15:42763800-42774600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:42763800-42775000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:42763800-42775000	Weak transcription	Fetal Thymus	thymus

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