Variant report

Variant	rs12134258
Chromosome Location	chr1:224412157-224412158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224406207..224408760-chr1:224411418..224413367,2	K562	blood:
2	chr1:224369856..224371888-chr1:224410575..224412569,2	K562	blood:
3	chr1:224410677..224413155-chr1:224413701..224415369,2	MCF-7	breast:
4	chr1:224410361..224412569-chr1:224413431..224415839,2	K562	blood:

Variant related genes	Relation type
ENSG00000237101	Chromatin interaction
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495222	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10753460	0.86[ASN][1000 genomes]
rs10753461	0.81[ASN][1000 genomes]
rs10799529	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799539	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799551	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[TSI][hapmap]
rs10799554	0.85[ASN][1000 genomes]
rs10916489	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs10916512	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10916515	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs10916533	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916534	0.89[ASN][1000 genomes]
rs10916535	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916543	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs12135557	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1401318	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1533589	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs1976788	0.90[ASN][1000 genomes]
rs2405302	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3767732	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs4290029	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4654009	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs4654010	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs6664230	0.95[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs6674695	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6682662	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72755906	0.80[AMR][1000 genomes]
rs72755909	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72755914	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72755915	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72755917	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541131	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs908803	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs908804	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][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	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12134258	FBXO28	cis	multi-tissue	Pritchard
rs12134258	DEGS1	cis	multi-tissue	Pritchard
rs12134258	FBXO28	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
3	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:224394000-224414600	Weak transcription	HMEC	breast
5	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
6	chr1:224399400-224414200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:224399400-224414200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:224401400-224413800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:224401400-224413800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:224401400-224414800	Weak transcription	Right Ventricle	heart
11	chr1:224401600-224414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:224401800-224415200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:224401800-224427600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
15	chr1:224402200-224413800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:224402200-224414200	Weak transcription	GM12878-XiMat	blood
17	chr1:224406000-224414200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:224406200-224413800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:224406200-224414200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:224406200-224414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:224406200-224414200	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:224406200-224414400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:224406400-224414200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:224406800-224414400	Weak transcription	Pancreas	Pancrea
28	chr1:224407200-224413800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:224407200-224414400	Weak transcription	Placenta	Placenta
30	chr1:224407600-224414200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:224407600-224414200	Weak transcription	Fetal Thymus	thymus
32	chr1:224407600-224414200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:224407600-224434000	Weak transcription	Fetal Brain Male	brain
34	chr1:224407800-224414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:224407800-224414200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:224407800-224414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:224408000-224414200	Weak transcription	Gastric	stomach
38	chr1:224410000-224412200	Enhancers	Stomach Mucosa	stomach
39	chr1:224410400-224414200	Weak transcription	Liver	Liver
40	chr1:224411000-224412200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:224411000-224412200	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr1:224411000-224412200	Enhancers	NH-A	brain
43	chr1:224411000-224412400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:224411000-224412400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:224411000-224412400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
46	chr1:224411000-224412400	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr1:224411000-224412400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:224411000-224412400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:224411000-224412400	Enhancers	Colon Smooth Muscle	Colon
50	chr1:224411000-224412400	Enhancers	Duodenum Mucosa	Duodenum

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