Variant report

Variant	rs2088514
Chromosome Location	chr1:222831372-222831373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:222829766-222841488	K562	blood:	n/a	n/a
2	STAT3	chr1:222831287-222831479	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:222830633-222831537	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222829835..222832236-chr1:222908968..222911331,2	K562	blood:
2	chr1:222816758..222818499-chr1:222830262..222833002,2	K562	blood:

Variant related genes	Relation type
MIA3	TF binding region
ENSG00000197520	Chromatin interaction
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11485123	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12063226	0.84[EUR][1000 genomes]
rs1391557	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1391558	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498382	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17011666	0.92[ASW][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs17011681	0.82[JPT][hapmap]
rs17011686	0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs17163358	0.82[JPT][hapmap]
rs17163450	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17163468	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17465637	0.86[JPT][hapmap]
rs1909195	0.81[AMR][1000 genomes]
rs1909197	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2030076	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2133188	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2133189	0.82[JPT][hapmap]
rs2270707	0.92[ASW][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2291832	0.82[JPT][hapmap]
rs2291834	0.82[JPT][hapmap]
rs2378604	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2936020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936023	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936049	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2936051	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2936052	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2936054	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3002129	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002146	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3002148	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008614	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3008615	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3008616	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008618	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008622	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3008625	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008629	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008637	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34433664	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35507977	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs3811465	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61827168	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2088514	C1orf58	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222818400-222833600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222818800-222841600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:222819000-222841800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:222819200-222841400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:222819200-222841600	Strong transcription	Placenta	Placenta
6	chr1:222819400-222841200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:222820000-222838800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:222820000-222841400	Strong transcription	HSMM	muscle
9	chr1:222820000-222841600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:222820200-222838800	Strong transcription	NHDF-Ad	bronchial
11	chr1:222820200-222841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:222820200-222841400	Strong transcription	NH-A	brain
13	chr1:222820400-222841800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:222820600-222841200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:222820600-222841400	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:222820800-222841000	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:222820800-222841200	Strong transcription	Fetal Intestine Large	intestine
18	chr1:222821000-222840000	Strong transcription	Fetal Kidney	kidney
19	chr1:222821200-222841400	Strong transcription	Adipose Nuclei	Adipose
20	chr1:222821400-222840000	Strong transcription	Fetal Brain Female	brain
21	chr1:222822200-222838800	Strong transcription	Colon Smooth Muscle	Colon
22	chr1:222822200-222841200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:222822200-222841400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:222822400-222841200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:222822400-222841400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:222822600-222840000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:222822600-222841400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:222822600-222841400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:222822800-222840800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:222823000-222838400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:222823000-222839200	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:222823000-222841200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:222823000-222841400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:222823200-222840000	Strong transcription	Brain Substantia Nigra	brain
35	chr1:222823200-222840600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:222823200-222841400	Strong transcription	HepG2	liver
37	chr1:222823200-222841400	Strong transcription	K562	blood
38	chr1:222823400-222831400	Weak transcription	Colonic Mucosa	Colon
39	chr1:222823400-222841400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:222824000-222839600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:222824000-222841400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:222824000-222841400	Strong transcription	A549	lung
43	chr1:222824200-222839800	Strong transcription	Fetal Lung	lung
44	chr1:222825000-222841400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:222825200-222839000	Strong transcription	Brain Cingulate Gyrus	brain
46	chr1:222825600-222840000	Strong transcription	Left Ventricle	heart
47	chr1:222825800-222839600	Strong transcription	Rectal Smooth Muscle	rectum
48	chr1:222826800-222841400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:222827000-222834000	Weak transcription	Right Ventricle	heart
50	chr1:222827000-222835400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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