Variant report

Variant	rs1809139
Chromosome Location	chr2:173982876-173982877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173972593..173975547-chr2:173981865..173984989,3	MCF-7	breast:
2	chr2:173942302..173944887-chr2:173980344..173983035,2	K562	blood:
3	chr2:173902260..173904041-chr2:173982798..173984543,2	MCF-7	breast:
4	chr2:173951489..173953627-chr2:173981191..173983390,3	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11680555	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11687539	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12463612	0.80[CEU][hapmap]
rs17710065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17710437	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2043950	0.83[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3754739	0.80[ASN][1000 genomes]
rs3754747	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3769159	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3769162	0.83[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs3769163	0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3820835	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4399689	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4972529	0.83[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4972532	0.82[ASN][1000 genomes]
rs56980119	0.80[ASN][1000 genomes]
rs62175824	0.82[ASN][1000 genomes]
rs6742219	0.80[CEU][hapmap]
rs6759847	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs722864	0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs734993	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73974105	0.82[ASN][1000 genomes]
rs746179	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7567355	0.82[CEU][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7575319	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7599340	0.87[CEU][hapmap]
rs7601536	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs935006	0.87[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs935007	0.93[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv834461	chr2:173979734-174038471	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1809139	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:173953800-173991400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:173955600-173984000	Weak transcription	Gastric	stomach
4	chr2:173957800-173983800	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:173958000-173983800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:173962200-173983800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:173965000-173987400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr2:173965400-173984400	Weak transcription	Aorta	Aorta
9	chr2:173965400-173987200	Weak transcription	Dnd41	blood
10	chr2:173965400-173989200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:173965600-173983800	Weak transcription	Adipose Nuclei	Adipose
12	chr2:173968600-173990600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:173969200-173987600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:173970000-173983200	Weak transcription	Right Atrium	heart
15	chr2:173971600-173985600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:173972200-173983800	Weak transcription	Lung	lung
17	chr2:173972600-173983800	Weak transcription	Right Ventricle	heart
18	chr2:173973200-173983800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:173974400-174005200	Weak transcription	Fetal Intestine Small	intestine
20	chr2:173974600-173983800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:173974600-173984000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:173974600-173984400	Weak transcription	NHEK	skin
23	chr2:173974800-173983000	Weak transcription	Fetal Heart	heart
24	chr2:173974800-173983000	Weak transcription	Osteobl	bone
25	chr2:173974800-173983200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:173974800-173983200	Weak transcription	NHDF-Ad	bronchial
27	chr2:173974800-173983800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:173974800-173984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:173974800-173988600	Weak transcription	HSMM	muscle
30	chr2:173974800-173991400	Weak transcription	K562	blood
31	chr2:173978200-173995200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:173980000-173985800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:173980600-173983200	Weak transcription	Psoas Muscle	Psoas
34	chr2:173980600-173989200	Weak transcription	Esophagus	oesophagus
35	chr2:173981000-174000800	Weak transcription	Fetal Thymus	thymus
36	chr2:173981400-173983000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:173981400-173983200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:173981600-173983000	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:173981800-173983600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:173981800-173983800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:173982200-173983200	Weak transcription	Ovary	ovary
42	chr2:173982400-173983800	Weak transcription	Left Ventricle	heart
43	chr2:173982600-173983000	Enhancers	A549	lung
44	chr2:173982600-173984000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:173982800-174006400	Weak transcription	Fetal Lung	lung

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