Variant report

Variant	rs3770459
Chromosome Location	chr2:172648592-172648593
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172648009..172650848-chr2:172967323..172968978,2	MCF-7	breast:
2	chr2:172637502..172642511-chr2:172648363..172652969,5	K562	blood:

Variant related genes	Relation type
ENSG00000236651	Chromatin interaction
ENSG00000115844	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11673831	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11675404	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11675891	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12991441	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13016580	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13017695	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13021138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024662	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1554259	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17427311	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17427473	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]
rs17499306	0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17499502	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17848721	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1996424	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2138349	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2357062	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34108287	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34221876	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34632749	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34962243	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35162284	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4581870	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs62182397	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62182402	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62184174	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72889853	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs74173119	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs979955	0.86[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
rs3770459	SLC25A12	cis	cerebellum	SCAN
rs3770459	B3GALT1	cis	cerebellum	SCAN
rs3770459	SLC25A12	cis	parietal	SCAN
rs3770459	MAP1D	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:172610200-172651400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:172635400-172654800	Weak transcription	A549	lung
4	chr2:172635600-172654600	Weak transcription	Liver	Liver
5	chr2:172636800-172654800	Weak transcription	Small Intestine	intestine
6	chr2:172638000-172650200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:172638600-172650600	Strong transcription	Stomach Smooth Muscle	stomach
8	chr2:172638800-172650400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:172638800-172650800	Strong transcription	Primary T cells from cord blood	blood
10	chr2:172638800-172650800	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:172638800-172651000	Strong transcription	Dnd41	blood
12	chr2:172639200-172650200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:172639200-172650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:172639800-172650200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:172639800-172650600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:172640000-172650400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:172640000-172650400	Strong transcription	Fetal Thymus	thymus
18	chr2:172640000-172651400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:172640200-172648600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:172640200-172648800	Strong transcription	GM12878-XiMat	blood
21	chr2:172640200-172650400	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:172640200-172650600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:172640200-172651000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:172640200-172662800	Weak transcription	Fetal Brain Male	brain
25	chr2:172640400-172668000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:172640600-172650600	Strong transcription	Left Ventricle	heart
27	chr2:172641000-172648800	Strong transcription	Thymus	Thymus
28	chr2:172641000-172650400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:172641000-172650400	Strong transcription	Fetal Stomach	stomach
30	chr2:172641600-172666400	Weak transcription	Fetal Kidney	kidney
31	chr2:172642000-172649800	Weak transcription	HMEC	breast
32	chr2:172642200-172651400	Weak transcription	Fetal Heart	heart
33	chr2:172642200-172651400	Weak transcription	Fetal Intestine Large	intestine
34	chr2:172642200-172654000	Weak transcription	HUVEC	blood vessel
35	chr2:172642200-172654600	Weak transcription	NHEK	skin
36	chr2:172642200-172654800	Weak transcription	HSMM	muscle
37	chr2:172642200-172663600	Weak transcription	K562	blood
38	chr2:172642200-172665800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:172642400-172688400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:172643600-172687800	Weak transcription	Hela-S3	cervix
41	chr2:172643800-172674600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:172644000-172650400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:172644000-172667000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:172644200-172649800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:172644200-172666600	Weak transcription	Placenta	Placenta
46	chr2:172644400-172649000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:172644400-172654800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:172644400-172655000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:172644400-172655000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:172644400-172656000	Weak transcription	Aorta	Aorta

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