Variant report

Variant	rs6694224
Chromosome Location	chr1:150061910-150061911
allele	G/T
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	SPI1	chr1:150061893-150062845	GM12878	blood:	n/a	chr1:150062431-150062444 chr1:150062450-150062457 chr1:150062431-150062444 chr1:150062285-150062292 chr1:150062448-150062461

No.	Distal block	Cell Line	Cell type
1	chr1:150039402..150041296-chr1:150061264..150063367,2	MCF-7	breast:
2	chr1:150053480..150056839-chr1:150057384..150063028,6	MCF-7	breast:
3	chr1:150053441..150055010-chr1:150059961..150062562,2	MCF-7	breast:
4	chr1:150059899..150062299-chr1:150132296..150134996,2	K562	blood:

Variant related genes	Relation type
VPS45	TF binding region
ENSG00000136631	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10749675	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10888570	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205334	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1531578	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1531579	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1531580	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2127135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3904949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926404	1.00[AMR][1000 genomes]
rs4926410	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6587749	1.00[AFR][1000 genomes]
rs6587750	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7518829	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9325998	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases
2	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6694224	C1orf54	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150040200-150090800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:150040400-150078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:150040400-150082800	Weak transcription	Small Intestine	intestine
4	chr1:150040400-150086800	Weak transcription	Esophagus	oesophagus
5	chr1:150040400-150121400	Weak transcription	Pancreas	Pancrea
6	chr1:150040600-150072200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:150040600-150092000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:150041000-150064000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:150041000-150114400	Weak transcription	Right Ventricle	heart
10	chr1:150041400-150066000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:150041400-150067800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:150041400-150069200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:150042200-150073400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:150042200-150086600	Weak transcription	Gastric	stomach
15	chr1:150042400-150063200	Weak transcription	NHEK	skin
16	chr1:150042400-150067600	Weak transcription	Psoas Muscle	Psoas
17	chr1:150042600-150090800	Weak transcription	Stomach Mucosa	stomach
18	chr1:150048400-150068400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:150048800-150064000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:150050200-150065600	Weak transcription	Fetal Brain Male	brain
21	chr1:150050400-150064000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:150050600-150067200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:150050600-150084800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:150051200-150065400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:150051600-150065400	Weak transcription	HSMMtube	muscle
26	chr1:150051800-150064000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:150052000-150071400	Weak transcription	Fetal Intestine Small	intestine
28	chr1:150052000-150116800	Weak transcription	Spleen	Spleen
29	chr1:150055000-150063800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:150055000-150086200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:150055000-150100600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:150055000-150120800	Weak transcription	Aorta	Aorta
33	chr1:150055200-150062000	Weak transcription	Fetal Heart	heart
34	chr1:150055200-150065600	Weak transcription	Colonic Mucosa	Colon
35	chr1:150055200-150069600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:150055200-150078400	Weak transcription	Thymus	Thymus
37	chr1:150055200-150096000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:150055200-150104800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:150055400-150065600	Weak transcription	Hela-S3	cervix
40	chr1:150055400-150067200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:150055600-150065600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:150055600-150076400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:150055800-150064400	Weak transcription	HepG2	liver
44	chr1:150056000-150072200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:150056200-150065600	Weak transcription	Brain Angular Gyrus	brain
46	chr1:150056200-150074200	Weak transcription	Lung	lung
47	chr1:150056200-150081800	Weak transcription	Brain Substantia Nigra	brain
48	chr1:150056400-150064000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:150056600-150062400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:150056600-150065400	Weak transcription	Colon Smooth Muscle	Colon

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