Variant report

Variant	rs4924678
Chromosome Location	chr15:42761436-42761437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1060291	0.85[CEU][hapmap]
rs1062038	0.89[YRI][hapmap]
rs10851410	0.90[CEU][hapmap]
rs10851411	0.85[CEU][hapmap]
rs11022	0.90[CEU][hapmap]
rs11070374	0.95[CEU][hapmap]
rs11636577	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11638208	0.91[EUR][1000 genomes]
rs12101559	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs12324717	0.90[CEU][hapmap]
rs12443246	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898937	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903432	0.81[EUR][1000 genomes]
rs12913324	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973265	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1900920	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900921	0.90[CEU][hapmap]
rs2241998	0.90[CEU][hapmap]
rs2255995	0.81[EUR][1000 genomes]
rs2412715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2595939	0.81[EUR][1000 genomes]
rs2595940	0.95[CEU][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2595941	0.80[EUR][1000 genomes]
rs2617235	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617236	0.95[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2617237	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617238	0.80[ASN][1000 genomes]
rs28886308	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899051	0.90[CEU][hapmap]
rs3986280	0.90[CEU][hapmap]
rs4573906	0.81[EUR][1000 genomes]
rs4923948	0.90[CEU][hapmap]
rs62022317	0.85[EUR][1000 genomes]
rs7169521	0.83[AFR][1000 genomes]
rs7169615	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023929	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8033412	0.90[CEU][hapmap]
rs8034232	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8034238	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036544	0.95[ASN][1000 genomes]
rs9302112	0.95[CEU][hapmap];0.82[TSI][hapmap];0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4924678	MAP1A	cis	parietal	SCAN
rs4924678	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs4924678	SNAP23	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42701200-42766600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:42737200-42764800	Weak transcription	A549	lung
3	chr15:42744200-42762200	Weak transcription	K562	blood
4	chr15:42744200-42763200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:42744200-42767000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:42744200-42781800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:42744200-42782400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:42749200-42761800	Weak transcription	Brain Germinal Matrix	brain
9	chr15:42749600-42764600	Weak transcription	Colonic Mucosa	Colon
10	chr15:42750000-42782600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:42750200-42763600	Weak transcription	Right Atrium	heart
12	chr15:42750200-42766400	Weak transcription	Right Ventricle	heart
13	chr15:42750200-42782400	Weak transcription	Aorta	Aorta
14	chr15:42750400-42761600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:42750400-42762800	Weak transcription	HMEC	breast
16	chr15:42750400-42765000	Weak transcription	Fetal Brain Male	brain
17	chr15:42750600-42761800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:42750600-42763200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:42750600-42766800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:42750800-42763400	Weak transcription	Psoas Muscle	Psoas
21	chr15:42750800-42764400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:42750800-42782400	Weak transcription	Ovary	ovary
23	chr15:42751000-42782400	Weak transcription	Fetal Lung	lung
24	chr15:42753200-42764000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:42753600-42764000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:42754200-42763200	Weak transcription	Fetal Heart	heart
27	chr15:42754200-42764600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:42754600-42764600	Weak transcription	Small Intestine	intestine
29	chr15:42754600-42782400	Weak transcription	HSMMtube	muscle
30	chr15:42755000-42763600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:42756000-42762800	Weak transcription	HSMM	muscle
32	chr15:42756000-42777600	Weak transcription	Lung	lung
33	chr15:42756000-42782600	Weak transcription	Esophagus	oesophagus
34	chr15:42756200-42782400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:42756600-42763600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:42757800-42763200	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:42757800-42782600	Weak transcription	Gastric	stomach
38	chr15:42758000-42764800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:42758000-42781600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:42758000-42782400	Weak transcription	NHLF	lung
41	chr15:42758200-42763000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:42758200-42763200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:42758200-42763200	Weak transcription	Dnd41	blood
44	chr15:42758200-42764400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:42758200-42766200	Weak transcription	NH-A	brain
46	chr15:42758200-42766600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:42758200-42766600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:42758200-42770600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:42758200-42770800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr15:42758200-42776200	Weak transcription	HepG2	liver

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