Variant report

Variant	rs1667275
Chromosome Location	chr18:29213265-29213266
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1026122	0.85[ASN][1000 genomes]
rs1026123	0.85[CEU][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1078998	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11663991	0.89[EUR][1000 genomes]
rs12962843	0.86[ASN][1000 genomes]
rs1612691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1621308	0.85[ASN][1000 genomes]
rs1667262	0.85[ASN][1000 genomes]
rs1667274	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1667276	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1667279	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667280	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667283	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1667286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1667287	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1791161	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1791169	0.81[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1791171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1791181	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1791221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2595360	0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs3764474	0.86[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3794878	0.81[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3794882	0.91[ASN][1000 genomes]
rs41447647	0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4799311	0.81[JPT][hapmap]
rs6506935	0.88[ASN][1000 genomes]
rs7242641	0.91[ASN][1000 genomes]
rs8097755	0.86[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs895888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974676	0.85[ASN][1000 genomes]
rs974677	0.85[ASN][1000 genomes]
rs9950458	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1667275	AQP4	cis	cerebellum	SCAN
rs1667275	DSC1	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29192400-29217400	Weak transcription	Left Ventricle	heart
2	chr18:29194800-29226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:29197600-29224800	Weak transcription	Brain Anterior Caudate	brain
4	chr18:29197600-29224800	Weak transcription	Brain Germinal Matrix	brain
5	chr18:29199800-29217200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr18:29200000-29222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr18:29200200-29222000	Weak transcription	HMEC	breast
8	chr18:29202800-29235000	Weak transcription	Pancreas	Pancrea
9	chr18:29202800-29240200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr18:29203200-29217000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:29203800-29220200	Weak transcription	Ovary	ovary
12	chr18:29203800-29226000	Weak transcription	Fetal Lung	lung
13	chr18:29203800-29227400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:29204000-29213600	Weak transcription	Thymus	Thymus
15	chr18:29204000-29228400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr18:29204200-29223200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:29204400-29220800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr18:29204400-29228400	Weak transcription	Psoas Muscle	Psoas
19	chr18:29204600-29213600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr18:29204600-29238600	Weak transcription	Gastric	stomach
21	chr18:29205000-29215600	Weak transcription	Fetal Stomach	stomach
22	chr18:29205000-29215800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr18:29205000-29227400	Weak transcription	A549	lung
24	chr18:29206800-29217000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr18:29206800-29225800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr18:29207600-29217600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr18:29208000-29227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr18:29208200-29223200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:29208400-29214000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr18:29208400-29214200	Weak transcription	Fetal Intestine Large	intestine
31	chr18:29208400-29227000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:29208400-29229000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr18:29208800-29218400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr18:29208800-29222600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr18:29209000-29217200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr18:29209000-29226000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr18:29209000-29228400	Weak transcription	Brain Angular Gyrus	brain
38	chr18:29210000-29223400	Weak transcription	Adipose Nuclei	Adipose
39	chr18:29210800-29224600	Weak transcription	Fetal Intestine Small	intestine
40	chr18:29211000-29213400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr18:29211000-29213400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr18:29211000-29213600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr18:29211000-29213600	Weak transcription	K562	blood
44	chr18:29211000-29214200	Weak transcription	Primary T cells from cord blood	blood
45	chr18:29211000-29216400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr18:29211000-29223200	Weak transcription	Fetal Brain Female	brain
47	chr18:29211000-29227400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr18:29211200-29213400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr18:29211200-29216400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr18:29211200-29216400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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