Variant report

Variant	rs3759792
Chromosome Location	chr15:43252764-43252765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10518779	1.00[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12898255	0.82[AMR][1000 genomes]
rs16957168	0.88[ASW][hapmap];0.95[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs16957422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs2176870	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs2412748	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28374998	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28494835	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28581361	0.81[AFR][1000 genomes]
rs28609797	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28613047	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28633493	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796057	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28810091	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28871732	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35838915	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4274403	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4924699	0.85[CEU][hapmap]
rs4924705	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs66947001	0.85[EUR][1000 genomes]
rs7166705	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7170376	0.83[AMR][1000 genomes]
rs7176957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7178248	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7181859	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7182141	0.88[ASW][hapmap];0.95[CEU][hapmap];0.92[MEX][hapmap]
rs7182650	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8028785	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs8036674	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037613	0.85[CEU][hapmap]
rs8041432	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9920061	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920182	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9920202	1.00[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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
6	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1036512	chr15:43164906-43274531	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv569239	chr15:43201109-43392075	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv1039587	chr15:43204351-43378274	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv1050987	chr15:43237103-43385515	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv542369	chr15:43237103-43385515	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	esv3421859	chr15:43249285-43280570	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3759792	MAP1A	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43232000-43362800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:43236000-43268400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:43237800-43254800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:43241200-43269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:43241600-43258600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr15:43241600-43258800	Strong transcription	Placenta	Placenta
7	chr15:43241600-43259200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr15:43241600-43259800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:43241600-43261800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:43241600-43271000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:43241600-43271800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:43241800-43254000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:43241800-43254400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr15:43241800-43257600	Strong transcription	Fetal Brain Female	brain
15	chr15:43241800-43258800	Strong transcription	Adipose Nuclei	Adipose
16	chr15:43241800-43258800	Strong transcription	Fetal Intestine Large	intestine
17	chr15:43241800-43259400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:43241800-43270800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr15:43242000-43254800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:43242000-43258800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:43242200-43253000	Strong transcription	Brain Anterior Caudate	brain
22	chr15:43242200-43253400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr15:43242200-43258600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:43242200-43258800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:43242200-43258800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr15:43242200-43259000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:43242200-43259400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:43242200-43270800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:43242400-43259000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr15:43242800-43262600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:43243200-43256200	Weak transcription	Fetal Heart	heart
32	chr15:43243600-43253000	Strong transcription	Primary B cells from cord blood	blood
33	chr15:43243800-43265000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:43244000-43276400	Weak transcription	Psoas Muscle	Psoas
35	chr15:43244600-43254600	Weak transcription	Small Intestine	intestine
36	chr15:43244600-43266200	Weak transcription	Gastric	stomach
37	chr15:43247400-43258800	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:43247400-43259000	Strong transcription	Liver	Liver
39	chr15:43247600-43253000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:43247600-43253000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:43247600-43258600	Strong transcription	Primary T cells from cord blood	blood
42	chr15:43247600-43258800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:43247600-43260800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:43247800-43258600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:43248000-43320600	Weak transcription	Stomach Mucosa	stomach
46	chr15:43248200-43253400	Strong transcription	Ovary	ovary
47	chr15:43248200-43257400	Strong transcription	Left Ventricle	heart
48	chr15:43248200-43259400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:43248200-43265000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:43248400-43255800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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