Variant report

Variant	rs10495222
Chromosome Location	chr1:224403769-224403770
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	chr1:224391181..224392775-chr1:224402864..224405337,2	K562	blood:
2	chr1:224370877..224372532-chr1:224401645..224404374,2	K562	blood:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10753460	0.86[ASN][1000 genomes]
rs10799529	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799539	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799551	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs10799554	0.83[ASN][1000 genomes]
rs10916468	0.81[ASN][1000 genomes]
rs10916489	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10916512	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10916515	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs10916533	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916534	0.87[ASN][1000 genomes]
rs10916535	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916543	0.91[CHB][hapmap]
rs12134258	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]
rs12135557	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12142842	0.82[ASN][1000 genomes]
rs12143450	0.80[ASN][1000 genomes]
rs1401318	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1533589	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1976788	0.88[ASN][1000 genomes]
rs2405302	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3767732	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs4290029	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4446934	0.82[ASN][1000 genomes]
rs4653997	0.81[ASN][1000 genomes]
rs4654009	0.95[CHB][hapmap];0.83[CHD][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap]
rs4654010	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs55977521	0.82[ASN][1000 genomes]
rs6664230	0.95[CHB][hapmap]
rs6674695	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682662	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72755906	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72755909	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72755914	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72755915	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72755917	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7541131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908802	0.82[ASN][1000 genomes]
rs908803	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs908804	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	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
3	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
rs10495222	DEGS1	cis	multi-tissue	Pritchard
rs10495222	FBXO28	cis	lymphoblastoid	seeQTL
rs10495222	FBXO28	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224393800-224405600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
5	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:224394000-224414600	Weak transcription	HMEC	breast
7	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
8	chr1:224399400-224406600	Weak transcription	Pancreas	Pancrea
9	chr1:224399400-224411000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:224399400-224414200	Weak transcription	Adipose Nuclei	Adipose
11	chr1:224399400-224414200	Weak transcription	Brain Anterior Caudate	brain
12	chr1:224399600-224405600	Weak transcription	Fetal Lung	lung
13	chr1:224400600-224406000	Weak transcription	Fetal Thymus	thymus
14	chr1:224401000-224406600	Weak transcription	Gastric	stomach
15	chr1:224401400-224406000	Weak transcription	Right Atrium	heart
16	chr1:224401400-224413800	Weak transcription	Primary B cells from cord blood	blood
17	chr1:224401400-224413800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:224401400-224414800	Weak transcription	Right Ventricle	heart
19	chr1:224401600-224405600	Weak transcription	Fetal Stomach	stomach
20	chr1:224401600-224406000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:224401600-224406000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:224401600-224414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:224401800-224405400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:224401800-224405600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:224401800-224405600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:224401800-224405600	Weak transcription	K562	blood
27	chr1:224401800-224405800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:224401800-224406600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:224401800-224406600	Weak transcription	Placenta	Placenta
30	chr1:224401800-224407000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:224401800-224407000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:224401800-224411000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:224401800-224411000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:224401800-224411000	Weak transcription	Small Intestine	intestine
35	chr1:224401800-224415200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:224401800-224427600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
38	chr1:224402200-224405800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:224402200-224405800	Weak transcription	Fetal Intestine Small	intestine
40	chr1:224402200-224406600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:224402200-224406600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:224402200-224406600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:224402200-224406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:224402200-224406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:224402200-224411000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:224402200-224413800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:224402200-224414200	Weak transcription	GM12878-XiMat	blood
48	chr1:224402400-224404200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:224402400-224405600	Weak transcription	Fetal Intestine Large	intestine
50	chr1:224402400-224405600	Weak transcription	Fetal Kidney	kidney

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