Variant report

Variant	rs158690
Chromosome Location	chr9:93656985-93656986
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	chr9:93655595..93658492-chr9:93659602..93661599,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12344755	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1675333	0.86[EUR][1000 genomes]
rs1755937	0.86[EUR][1000 genomes]
rs1755938	0.83[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2780709	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs290205	0.95[TSI][hapmap]
rs290221	0.83[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs290222	0.86[EUR][1000 genomes]
rs290226	0.83[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs290228	0.83[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs290255	0.83[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs3887261	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active 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
3	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1053252	chr9:93610132-93699103	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs158690	WNK2	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93634000-93666200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:93641200-93657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:93643000-93666600	Weak transcription	Stomach Mucosa	stomach
4	chr9:93643200-93663400	Weak transcription	Adipose Nuclei	Adipose
5	chr9:93643600-93665400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:93646200-93664800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:93646800-93657000	Weak transcription	NHEK	skin
8	chr9:93647200-93663400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr9:93647400-93666600	Strong transcription	Primary B cells from cord blood	blood
10	chr9:93647600-93662000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:93647600-93664800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:93647800-93662000	Strong transcription	Fetal Thymus	thymus
13	chr9:93648000-93662400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr9:93648200-93663200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:93648200-93665000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:93648600-93661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:93648800-93663200	Strong transcription	Thymus	Thymus
18	chr9:93650000-93660800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr9:93650000-93661200	Strong transcription	Fetal Intestine Small	intestine
20	chr9:93650000-93661400	Strong transcription	Fetal Stomach	stomach
21	chr9:93650000-93662600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr9:93651600-93657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:93651600-93661600	Weak transcription	Fetal Kidney	kidney
24	chr9:93651600-93664200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:93652600-93667200	Weak transcription	Gastric	stomach
26	chr9:93652800-93657600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:93652800-93657600	Weak transcription	Colonic Mucosa	Colon
28	chr9:93653000-93658800	Weak transcription	Esophagus	oesophagus
29	chr9:93653200-93657800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:93653400-93658000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:93654000-93662000	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:93654000-93662200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr9:93654000-93663200	Strong transcription	Spleen	Spleen
34	chr9:93654600-93657800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr9:93655400-93657600	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:93655400-93657600	Weak transcription	Lung	lung
37	chr9:93655400-93658200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:93655400-93663200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:93655400-93664000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:93655800-93657200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:93655800-93657600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:93655800-93657800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:93655800-93657800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr9:93655800-93657800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:93656000-93658000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr9:93656000-93658000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr9:93656200-93657200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:93656200-93657600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr9:93656200-93657800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:93656200-93657800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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