Variant report

Variant	rs17180749
Chromosome Location	chr12:104273718-104273719
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	chr12:104272930..104275342-chr12:104282013..104284611,2	K562	blood:
2	chr12:104271327..104273911-chr12:104324205..104326173,2	K562	blood:

Variant related genes	Relation type
ENSG00000166598	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12422615	1.00[MKK][hapmap]
rs12426161	1.00[EUR][1000 genomes]
rs12426183	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12426202	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12426220	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12582800	0.94[CEU][hapmap];1.00[EUR][1000 genomes]
rs1550207	1.00[MKK][hapmap]
rs17034637	1.00[MKK][hapmap]
rs17034639	1.00[MKK][hapmap]
rs17034640	1.00[MKK][hapmap]
rs17034642	1.00[MKK][hapmap]
rs17034645	1.00[MKK][hapmap]
rs17034648	1.00[MKK][hapmap]
rs17034662	1.00[MKK][hapmap]
rs17034880	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs17034914	1.00[CEU][hapmap]
rs17035153	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs17192854	1.00[MKK][hapmap]
rs17794246	1.00[MKK][hapmap]
rs17795280	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17795947	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1882019	1.00[MKK][hapmap]
rs2293626	1.00[MKK][hapmap]
rs35193500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3751207	1.00[MKK][hapmap]
rs3751208	1.00[MKK][hapmap]
rs3829300	1.00[MKK][hapmap]
rs4135065	1.00[AFR][1000 genomes]
rs4135082	1.00[MKK][hapmap]
rs4135085	1.00[MKK][hapmap]
rs4135087	1.00[MKK][hapmap]
rs55780086	1.00[AFR][1000 genomes]
rs55919036	1.00[EUR][1000 genomes]
rs728167	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9788014	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs9788136	1.00[CEU][hapmap]

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	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17180749	GNN	cis	parietal	SCAN
rs17180749	NT5DC3	cis	parietal	SCAN
rs17180749	GLT8D2	cis	parietal	SCAN
rs17180749	NFYB	cis	cerebellum	SCAN
rs17180749	HCFC2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104254800-104278200	Weak transcription	Aorta	Aorta
2	chr12:104271600-104274400	Enhancers	GM12878-XiMat	blood
3	chr12:104271800-104274000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:104271800-104275600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:104272200-104274000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:104272200-104274000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:104272200-104274000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:104272200-104274000	Weak transcription	HUVEC	blood vessel
9	chr12:104272200-104274200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:104272200-104276800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:104272200-104278200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:104272400-104273800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:104272400-104274000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:104272400-104274000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:104272400-104274200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:104272400-104275800	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:104272600-104273800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:104272600-104274000	Weak transcription	Fetal Thymus	thymus
19	chr12:104272600-104274200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:104272600-104274200	Weak transcription	Fetal Intestine Large	intestine
21	chr12:104272600-104274200	Weak transcription	A549	lung
22	chr12:104272800-104274000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:104272800-104275200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:104273200-104274200	Bivalent Enhancer	HepG2	liver
25	chr12:104273200-104277400	Enhancers	HMEC	breast
26	chr12:104273400-104277200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:104273400-104277600	Enhancers	NHEK	skin
28	chr12:104273600-104274400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:104273600-104275000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:104273600-104275400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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