Variant report

Variant	rs17427473
Chromosome Location	chr2:172576011-172576012
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	chr2:172575251..172577078-chr2:172966715..172969569,2	K562	blood:

Variant related genes	Relation type
ENSG00000236651	Chromatin interaction
ENSG00000115844	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11673831	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11675404	1.00[ASW][hapmap];0.83[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11675891	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12991441	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13016580	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13017695	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13021138	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13024662	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1554259	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17427311	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17499306	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17499502	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17848721	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1996424	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2138349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2357062	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34108287	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34221876	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34632749	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34962243	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35162284	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3770459	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62182397	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs62184174	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72889853	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74173119	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs979955	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17427473	B3GALT1	cis	cerebellum	SCAN
rs17427473	SLC25A12	cis	cerebellum	SCAN
rs17427473	MAP1D	cis	parietal	SCAN
rs17427473	SLC25A12	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545000-172580200	Weak transcription	Pancreas	Pancrea
2	chr2:172545000-172580400	Weak transcription	Spleen	Spleen
3	chr2:172545000-172580800	Weak transcription	Gastric	stomach
4	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:172545400-172588000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:172545800-172588000	Weak transcription	Right Ventricle	heart
7	chr2:172546600-172602800	Weak transcription	Small Intestine	intestine
8	chr2:172547000-172578600	Weak transcription	Fetal Brain Male	brain
9	chr2:172548400-172579600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:172551600-172584400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:172552200-172587600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:172554000-172580200	Weak transcription	Aorta	Aorta
13	chr2:172554400-172588000	Weak transcription	Esophagus	oesophagus
14	chr2:172554800-172580400	Weak transcription	K562	blood
15	chr2:172555000-172580200	Weak transcription	Brain Anterior Caudate	brain
16	chr2:172557400-172584400	Weak transcription	Ovary	ovary
17	chr2:172558800-172583400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:172559000-172585000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:172559600-172605200	Weak transcription	Colonic Mucosa	Colon
20	chr2:172560000-172576200	Weak transcription	Thymus	Thymus
21	chr2:172560400-172580800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:172561000-172579600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:172561000-172583600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:172561200-172580200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:172561200-172587800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:172561400-172580200	Weak transcription	Brain Substantia Nigra	brain
27	chr2:172561400-172601800	Weak transcription	Fetal Heart	heart
28	chr2:172563200-172583000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:172563800-172583400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:172564200-172610000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:172564800-172576800	Weak transcription	Brain Germinal Matrix	brain
32	chr2:172567000-172584200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:172569000-172584200	Weak transcription	Dnd41	blood
34	chr2:172569000-172618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:172569200-172578400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:172569200-172579600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:172569200-172582400	Weak transcription	A549	lung
38	chr2:172569200-172583400	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:172569200-172583600	Weak transcription	Hela-S3	cervix
40	chr2:172569400-172580400	Weak transcription	NHLF	lung
41	chr2:172569600-172580400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:172569800-172611400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:172570600-172580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:172571200-172579200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:172571400-172577400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:172571400-172577400	Strong transcription	Primary B cells from cord blood	blood
47	chr2:172571400-172577400	Strong transcription	Placenta	Placenta
48	chr2:172571400-172579000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:172571400-172579400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:172571400-172597800	Strong transcription	HSMM	muscle

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