Variant report

Variant	rs2285176
Chromosome Location	chr1:172421744-172421745
allele	C/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	TEAD4	chr1:172421567-172422160	K562	blood:	n/a	n/a
2	MAX	chr1:172421611-172421863	K562	blood:	n/a	chr1:172421769-172421778
3	TBL1XR1	chr1:172421669-172422251	K562	blood:	n/a	n/a
4	MAFF	chr1:172421603-172421924	K562	blood:	n/a	n/a
5	TEAD4	chr1:172421729-172422187	K562	blood:	n/a	n/a
6	CUX1	chr1:172421553-172421746	K562	blood:	n/a	n/a
7	MAZ	chr1:172421442-172421833	K562	blood:	n/a	chr1:172421769-172421778
8	JUND	chr1:172421496-172422185	K562	blood:	n/a	chr1:172421770-172421778 chr1:172421769-172421780 chr1:172421768-172421780
9	RCOR1	chr1:172421671-172422165	K562	blood:	n/a	n/a
10	TBP	chr1:172421565-172421904	K562	blood:	n/a	n/a
11	NR2F2	chr1:172421642-172422248	K562	blood:	n/a	n/a
12	UBTF	chr1:172421700-172422029	K562	blood:	n/a	n/a
13	UBTF	chr1:172421592-172421792	K562	blood:	n/a	n/a
14	EP300	chr1:172421663-172422119	K562	blood:	n/a	n/a
15	MAFK	chr1:172421647-172422135	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
2	chr1:172416845..172420491-chr1:172421660..172424212,3	MCF-7	breast:
3	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:

Variant related genes	Relation type
C1orf105	TF binding region
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1063412	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10752946	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs10752957	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs10798005	0.95[CHB][hapmap]
rs11484605	0.83[ASN][1000 genomes]
rs13932	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2157450	0.81[CHB][hapmap]
rs2213740	0.82[CHB][hapmap]
rs2269613	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2269614	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2269615	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2269616	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2285170	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285171	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2285172	1.00[ASN][1000 genomes]
rs2285173	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2285174	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2285175	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2301455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2422141	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2901656	0.96[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs3213563	0.95[ASN][1000 genomes]
rs3937046	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4916186	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4916258	0.95[ASN][1000 genomes]
rs60302909	0.92[ASN][1000 genomes]
rs6424923	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6658843	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs6673869	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6674073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6680035	0.81[CHB][hapmap]
rs6689377	1.00[ASN][1000 genomes]
rs6691993	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6699095	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs6702667	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs7411767	0.83[ASN][1000 genomes]
rs7516301	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs7550016	0.84[CHB][hapmap]
rs9286858	0.82[CHB][hapmap]
rs929098	1.00[ASN][1000 genomes]
rs9425308	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs9425311	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs9425313	0.80[ASN][1000 genomes]
rs9425316	0.82[ASN][1000 genomes]
rs9425329	0.81[CHB][hapmap]
rs9425334	0.81[CHB][hapmap]
rs9425598	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs9425600	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs9425601	0.81[ASN][1000 genomes]
rs9425602	0.80[ASN][1000 genomes]
rs9425604	0.80[ASN][1000 genomes]
rs9425606	0.95[CHB][hapmap];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947449	chr1:172419586-172424910	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2285176	PIGC	cis	Whole Blood	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172413600-172421800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:172413600-172421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:172417200-172421800	Weak transcription	Psoas Muscle	Psoas
4	chr1:172417200-172423200	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr1:172418000-172422200	Enhancers	NH-A	brain
6	chr1:172419400-172422200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:172419600-172422000	Weak transcription	Right Ventricle	heart
8	chr1:172419600-172423200	Enhancers	K562	blood
9	chr1:172419600-172426000	Enhancers	Fetal Intestine Large	intestine
10	chr1:172419800-172424400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:172420000-172421800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:172420200-172426000	Enhancers	Fetal Intestine Small	intestine
13	chr1:172420400-172421800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:172420400-172421800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:172420400-172421800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:172420400-172421800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:172420400-172422000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:172420400-172422400	Enhancers	Hela-S3	cervix
19	chr1:172420400-172422800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:172420400-172425400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:172420600-172421800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:172420600-172422800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:172420800-172422800	Enhancers	HepG2	liver
24	chr1:172421000-172422600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:172421200-172423000	Enhancers	A549	lung
26	chr1:172421200-172423200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:172421200-172423600	Enhancers	Fetal Heart	heart
28	chr1:172421400-172422000	Enhancers	Fetal Muscle Leg	muscle
29	chr1:172421400-172422000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:172421400-172422000	Enhancers	HSMMtube	muscle
31	chr1:172421400-172422400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:172421400-172422400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:172421400-172423200	Enhancers	Stomach Mucosa	stomach
34	chr1:172421600-172421800	Enhancers	Right Atrium	heart
35	chr1:172421600-172422000	Enhancers	HSMM	muscle
36	chr1:172421600-172422400	Enhancers	Placenta	Placenta
37	chr1:172421600-172422400	Enhancers	Gastric	stomach
38	chr1:172421600-172422400	Enhancers	Left Ventricle	heart
39	chr1:172421600-172422400	Enhancers	Pancreas	Pancrea
40	chr1:172421600-172422600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:172421600-172422600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:172421600-172422600	Enhancers	Skeletal Muscle Male	skeletal muscle

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