Variant report

Variant	rs35507977
Chromosome Location	chr1:222874118-222874119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222826589..222829229-chr1:222873150..222875151,2	K562	blood:
2	chr1:222873094..222876975-chr1:222880939..222885044,7	K562	blood:
3	chr1:222872226..222874267-chr1:222888403..222891368,2	K562	blood:
4	chr1:222871278..222875101-chr1:222884035..222886830,3	MCF-7	breast:
5	chr1:222871989..222876975-chr1:222881240..222885044,5	K562	blood:
6	chr1:222861525..222864468-chr1:222870086..222874487,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162819	Chromatin interaction
ENSG00000263877	Chromatin interaction
ENSG00000186063	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11485123	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12063226	0.87[EUR][1000 genomes]
rs1391557	0.81[EUR][1000 genomes]
rs1391558	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1498382	0.81[EUR][1000 genomes]
rs17011666	0.90[MEX][hapmap]
rs17011686	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs17163337	0.85[JPT][hapmap]
rs17163450	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs17163468	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs2030076	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2088514	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]
rs2133188	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2270707	0.95[MEX][hapmap]
rs2378604	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2936020	0.81[EUR][1000 genomes]
rs2936023	0.81[EUR][1000 genomes]
rs2936049	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];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3002146	0.81[EUR][1000 genomes]
rs3002148	0.81[EUR][1000 genomes]
rs3008622	0.82[AFR][1000 genomes]
rs3008625	0.81[EUR][1000 genomes]
rs3008629	0.86[AFR][1000 genomes]
rs3008637	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34433664	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6683071	0.80[ASW][hapmap]

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
rs35507977	C1orf58	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222835200-222884600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222839000-222877400	Weak transcription	Psoas Muscle	Psoas
3	chr1:222839000-222884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:222839600-222884600	Weak transcription	Esophagus	oesophagus
5	chr1:222840000-222884600	Weak transcription	Colonic Mucosa	Colon
6	chr1:222841200-222883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:222841400-222883200	Weak transcription	Fetal Heart	heart
8	chr1:222845000-222884600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:222849200-222875600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:222849400-222875400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:222849400-222883200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:222849600-222877800	Weak transcription	Fetal Brain Female	brain
13	chr1:222852400-222883800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:222854000-222875600	Weak transcription	NHLF	lung
15	chr1:222855200-222884600	Weak transcription	Pancreas	Pancrea
16	chr1:222855600-222883800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:222860000-222884600	Weak transcription	Left Ventricle	heart
18	chr1:222860200-222874400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:222860200-222875600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:222860200-222875600	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:222860200-222875600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:222860200-222875600	Weak transcription	NHEK	skin
23	chr1:222860200-222877400	Weak transcription	A549	lung
24	chr1:222860200-222883000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:222860200-222883000	Weak transcription	Hela-S3	cervix
26	chr1:222860200-222883200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:222860200-222883600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:222860200-222883800	Weak transcription	Fetal Kidney	kidney
29	chr1:222860200-222884000	Weak transcription	Brain Angular Gyrus	brain
30	chr1:222860200-222884200	Weak transcription	Brain Substantia Nigra	brain
31	chr1:222860200-222884400	Weak transcription	Placenta	Placenta
32	chr1:222860200-222884600	Weak transcription	Aorta	Aorta
33	chr1:222860200-222884600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:222860200-222884600	Weak transcription	Gastric	stomach
35	chr1:222860200-222884600	Weak transcription	Lung	lung
36	chr1:222860400-222877600	Weak transcription	HSMMtube	muscle
37	chr1:222860600-222880600	Weak transcription	Ovary	ovary
38	chr1:222860600-222882400	Weak transcription	Small Intestine	intestine
39	chr1:222860600-222884200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:222860800-222875400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:222861000-222885000	Weak transcription	Spleen	Spleen
42	chr1:222864600-222877400	Weak transcription	Fetal Lung	lung
43	chr1:222864800-222875600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:222866000-222875400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:222866600-222883000	Weak transcription	Fetal Brain Male	brain
46	chr1:222866800-222883800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:222867000-222874200	Weak transcription	NH-A	brain
48	chr1:222867200-222882600	Weak transcription	HepG2	liver
49	chr1:222867600-222874600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:222869200-222877600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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