Variant report

Variant	rs1217401
Chromosome Location	chr1:114438951-114438952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114437436..114439941-chr1:114469185..114470816,2	MCF-7	breast:
2	chr1:114417201..114419873-chr1:114437424..114440357,2	MCF-7	breast:
3	chr1:114429070..114435293-chr1:114435414..114441720,10	MCF-7	breast:
4	chr1:114432806..114434603-chr1:114437271..114439473,2	K562	blood:
5	chr1:114422775..114424966-chr1:114437779..114439803,2	K562	blood:
6	chr1:114418607..114420693-chr1:114436996..114439745,2	K562	blood:
7	chr1:114428650..114430928-chr1:114437544..114439159,2	K562	blood:

Variant related genes	Relation type
ENSG00000188761	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11102678	0.90[JPT][hapmap]
rs11102695	0.86[CEU][hapmap]
rs1217375	0.90[JPT][hapmap];0.82[MEX][hapmap]
rs1217382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1217393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217397	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217400	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217403	0.90[JPT][hapmap]
rs1217408	0.90[JPT][hapmap]
rs1217414	0.86[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs1217423	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230681	0.90[JPT][hapmap]
rs1310183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935836	0.90[JPT][hapmap]
rs1970559	0.90[JPT][hapmap]
rs2040041	0.90[JPT][hapmap]
rs2185827	0.90[JPT][hapmap]
rs2476599	0.90[JPT][hapmap]
rs2476602	0.90[JPT][hapmap];0.82[MEX][hapmap]
rs3789597	0.90[JPT][hapmap]
rs971173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1217401	AP4B1	cis	multi-tissue	Pritchard
rs1217401	BCL2L15	cis	cerebellum	SCAN
rs1217401	AP4B1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114420200-114446400	Weak transcription	Aorta	Aorta
3	chr1:114424600-114442400	Weak transcription	Psoas Muscle	Psoas
4	chr1:114430000-114440000	Weak transcription	Pancreas	Pancrea
5	chr1:114430000-114442400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:114430400-114440000	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:114430800-114440200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:114431800-114445400	Weak transcription	Stomach Mucosa	stomach
9	chr1:114434800-114440000	Weak transcription	Gastric	stomach
10	chr1:114434800-114440400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:114434800-114446200	Weak transcription	Fetal Heart	heart
12	chr1:114435600-114446200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:114435600-114446400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:114435800-114440400	Weak transcription	Fetal Kidney	kidney
15	chr1:114435800-114444400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:114436000-114444600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:114436000-114446800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:114436200-114441000	Strong transcription	Ovary	ovary
19	chr1:114436200-114442200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:114436200-114444600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:114436200-114444600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr1:114436200-114445200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:114436200-114446600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:114436200-114446600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:114436400-114439200	Strong transcription	Brain Substantia Nigra	brain
26	chr1:114436400-114439400	Strong transcription	Primary hematopoietic stem cells	blood
27	chr1:114436400-114440600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:114436400-114441000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:114436400-114442200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:114436400-114443800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:114436400-114444200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:114436400-114444600	Strong transcription	Primary T cells from cord blood	blood
33	chr1:114436400-114445000	Strong transcription	Liver	Liver
34	chr1:114436400-114445200	Strong transcription	Brain Anterior Caudate	brain
35	chr1:114436400-114445600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:114436600-114440800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:114436600-114441400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:114436600-114441600	Strong transcription	Adipose Nuclei	Adipose
39	chr1:114436600-114444600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:114436600-114445600	Strong transcription	Fetal Thymus	thymus
41	chr1:114436800-114439000	Strong transcription	NHLF	lung
42	chr1:114436800-114439400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:114436800-114440800	Strong transcription	Fetal Brain Female	brain
44	chr1:114436800-114441400	Strong transcription	HSMM	muscle
45	chr1:114436800-114441800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:114436800-114443800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:114436800-114444400	Strong transcription	Dnd41	blood
48	chr1:114436800-114445200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:114436800-114445600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:114436800-114445600	Strong transcription	Osteobl	bone

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