Variant report

Variant	rs1574257
Chromosome Location	chr2:173373190-173373191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173372610..173374163-chr2:173375837..173378337,2	K562	blood:

Variant related genes	Relation type
ENSG00000225205	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10174809	0.94[ASW][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10181851	0.84[CEU][hapmap]
rs12052479	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12469537	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13398175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34871211	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35022330	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765065	0.85[CEU][hapmap]
rs3792259	0.81[YRI][hapmap]
rs4075604	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55966259	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56832945	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61194385	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6730763	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7562753	0.83[EUR][1000 genomes]
rs7562865	0.83[EUR][1000 genomes]
rs7596665	0.81[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1574257	ZAK	cis	cerebellum	SCAN
rs1574257	GAD1	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173330600-173373200	Strong transcription	NHEK	skin
2	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
6	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:173331000-173373800	Strong transcription	HMEC	breast
9	chr2:173347800-173376200	Weak transcription	Fetal Heart	heart
10	chr2:173352000-173374200	Weak transcription	Fetal Lung	lung
11	chr2:173356400-173379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:173356600-173375400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:173356800-173374600	Weak transcription	Fetal Kidney	kidney
14	chr2:173356800-173376000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:173356800-173376200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:173357000-173376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:173357000-173376000	Weak transcription	Aorta	Aorta
18	chr2:173357200-173376600	Weak transcription	Right Ventricle	heart
19	chr2:173357600-173376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:173358000-173376200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:173361000-173375600	Weak transcription	Spleen	Spleen
22	chr2:173361200-173373600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:173361200-173375200	Weak transcription	GM12878-XiMat	blood
24	chr2:173361800-173373400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:173366200-173374400	Strong transcription	HSMM	muscle
26	chr2:173367400-173376000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:173367600-173374400	Weak transcription	Colonic Mucosa	Colon
28	chr2:173368600-173374400	Strong transcription	HSMMtube	muscle
29	chr2:173369400-173374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:173369600-173373400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:173369600-173374200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:173369600-173374800	Weak transcription	HepG2	liver
33	chr2:173369600-173375000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:173369600-173375400	Weak transcription	Left Ventricle	heart
35	chr2:173369600-173375600	Weak transcription	Liver	Liver
36	chr2:173369600-173376000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:173369600-173376000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:173369600-173376000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:173369600-173376000	Weak transcription	Esophagus	oesophagus
40	chr2:173369600-173376000	Weak transcription	HUVEC	blood vessel
41	chr2:173369800-173374400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:173369800-173375600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:173369800-173375600	Weak transcription	Adipose Nuclei	Adipose
44	chr2:173369800-173376600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:173370000-173375000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:173370200-173374200	Strong transcription	Primary T cells from cord blood	blood
47	chr2:173370200-173375000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:173370200-173375400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:173370200-173375600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:173370400-173374800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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