Variant report

Variant	rs3769173
Chromosome Location	chr2:174050988-174050989
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11680555	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11687539	0.85[ASN][1000 genomes]
rs17710065	0.85[ASN][1000 genomes]
rs17710437	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2043950	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2358088	0.97[ASN][1000 genomes]
rs3754739	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769159	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769162	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3769163	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4399689	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4972532	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56980119	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59500540	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61264428	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62175824	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs722864	0.83[ASN][1000 genomes]
rs734993	0.88[ASN][1000 genomes]
rs73974105	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs746179	0.88[ASN][1000 genomes]
rs7567355	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7575319	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7601536	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs935006	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935007	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3769173	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
2	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
3	chr2:174028400-174054600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:174030000-174052200	Weak transcription	Fetal Lung	lung
5	chr2:174037000-174053000	Weak transcription	Right Atrium	heart
6	chr2:174037400-174054600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:174045400-174052800	Weak transcription	Adipose Nuclei	Adipose
8	chr2:174046200-174054200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:174046200-174054400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:174046200-174055800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:174046400-174075800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:174046600-174055800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:174046800-174052800	Weak transcription	Fetal Intestine Small	intestine
14	chr2:174047000-174062800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:174047200-174052600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:174047600-174056400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:174047600-174060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:174047600-174062800	Weak transcription	GM12878-XiMat	blood
19	chr2:174047800-174065800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:174048400-174051000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:174048600-174095200	Weak transcription	Thymus	Thymus
22	chr2:174049000-174070600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:174049200-174051200	Enhancers	Fetal Heart	heart
24	chr2:174049200-174053000	Weak transcription	Brain Anterior Caudate	brain
25	chr2:174049200-174053600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:174049200-174070200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:174049200-174083200	Weak transcription	Small Intestine	intestine
28	chr2:174049400-174051600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:174049400-174051600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:174049400-174051800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:174049400-174051800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:174049400-174051800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:174049400-174051800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:174049400-174051800	Weak transcription	K562	blood
35	chr2:174049400-174052600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:174049400-174052600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:174049400-174052800	Weak transcription	Liver	Liver
38	chr2:174049400-174052800	Weak transcription	Ovary	ovary
39	chr2:174049400-174052800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:174049400-174053200	Weak transcription	Pancreas	Pancrea
41	chr2:174049400-174054200	Weak transcription	Fetal Intestine Large	intestine
42	chr2:174049400-174054800	Weak transcription	Dnd41	blood
43	chr2:174049400-174055800	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:174049400-174056000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:174049400-174058400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:174049400-174060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:174049400-174060800	Weak transcription	Lung	lung
48	chr2:174049400-174060800	Weak transcription	Right Ventricle	heart
49	chr2:174049400-174078200	Weak transcription	HUVEC	blood vessel
50	chr2:174049600-174051000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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