Variant report

Variant	rs1063412
Chromosome Location	chr1:172410967-172410968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:172406955-172411331	K562	blood:	n/a	n/a
2	STAT1	chr1:172410931-172412061	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:172410326..172414934-chr1:172499314..172504781,7	K562	blood:
2	chr1:172408347..172411338-chr1:172505750..172507919,2	K562	blood:
3	chr1:172405801..172407764-chr1:172408812..172411180,2	K562	blood:
4	chr1:172396564..172399537-chr1:172408525..172411857,4	K562	blood:
5	chr1:172397474..172399263-chr1:172409397..172412332,2	MCF-7	breast:
6	chr1:172406341..172410996-chr1:172411275..172416251,7	K562	blood:
7	chr1:172407211..172410996-chr1:172411275..172415406,7	K562	blood:

No data

Variant related genes	Relation type
C1orf105	TF binding region
ENSG00000135845	Chromatin interaction
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1014928	1.00[YRI][hapmap]
rs10752946	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs10752957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10798005	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10798026	0.87[ASW][hapmap]
rs10911786	0.87[ASW][hapmap]
rs11484605	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12076560	0.81[EUR][1000 genomes]
rs13932	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16844474	1.00[YRI][hapmap]
rs16844498	1.00[YRI][hapmap]
rs16844500	1.00[YRI][hapmap]
rs16844502	1.00[YRI][hapmap]
rs16844519	1.00[YRI][hapmap]
rs16844585	1.00[YRI][hapmap]
rs2157450	0.81[CHB][hapmap]
rs2213740	0.81[CHB][hapmap]
rs2269613	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2269614	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2269615	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269616	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs2285170	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2285171	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2285172	0.95[ASN][1000 genomes]
rs2285173	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2285174	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2285175	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2285176	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2301455	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2422141	0.85[ASN][1000 genomes]
rs2901656	0.81[CHB][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap]
rs3213563	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3937046	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4916186	0.84[ASN][1000 genomes]
rs4916258	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60302909	0.97[ASN][1000 genomes]
rs6424923	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6658843	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs6673869	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6674073	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6680035	0.81[CHB][hapmap]
rs6689377	0.95[ASN][1000 genomes]
rs6699095	0.81[CHB][hapmap]
rs6702667	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs7411767	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7516301	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs7528296	0.87[ASW][hapmap]
rs7550016	0.84[CHB][hapmap]
rs9286858	0.81[CHB][hapmap]
rs929098	0.95[ASN][1000 genomes]
rs9425308	0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs9425311	0.87[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs9425313	0.82[ASN][1000 genomes]
rs9425316	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425329	0.81[CHB][hapmap]
rs9425334	0.81[CHB][hapmap]
rs9425598	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs9425600	0.95[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs9425601	0.81[ASN][1000 genomes]
rs9425602	0.82[ASN][1000 genomes]
rs9425604	0.82[ASN][1000 genomes]
rs9425606	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1063412	C1orf105	cis	cerebellum	SCAN
rs1063412	PIGC	cis	brain	BrainEAC
rs1063412	PIGC	cis	Whole Blood	GTEx
rs1063412	SNORD47	cis	cerebellum	SCAN
rs1063412	SNORD79	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172373000-172411800	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172385800-172411000	Weak transcription	Fetal Stomach	stomach
3	chr1:172391000-172412200	Weak transcription	HSMMtube	muscle
4	chr1:172391800-172411000	Weak transcription	Spleen	Spleen
5	chr1:172392000-172412200	Weak transcription	Right Ventricle	heart
6	chr1:172392200-172411000	Weak transcription	Left Ventricle	heart
7	chr1:172395600-172412200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:172396200-172412000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:172396600-172411000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:172396600-172412400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:172396800-172411600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:172396800-172412200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:172397000-172411000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:172398800-172411000	Weak transcription	Aorta	Aorta
15	chr1:172399000-172411600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:172401200-172411000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:172401200-172411000	Weak transcription	Right Atrium	heart
18	chr1:172401200-172412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:172401400-172411000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:172401400-172411000	Weak transcription	HMEC	breast
21	chr1:172401400-172411800	Weak transcription	Fetal Intestine Small	intestine
22	chr1:172401400-172412000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:172401400-172412000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:172401400-172412200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:172401400-172412800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:172401600-172411000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:172401600-172411000	Weak transcription	Esophagus	oesophagus
28	chr1:172401600-172411000	Weak transcription	Placenta	Placenta
29	chr1:172401600-172411000	Weak transcription	Pancreas	Pancrea
30	chr1:172401600-172411000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:172401600-172411200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:172401600-172411800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:172401600-172412000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:172401600-172412200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:172402000-172412200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:172402200-172411400	Weak transcription	HepG2	liver
37	chr1:172405400-172411000	Weak transcription	Brain Anterior Caudate	brain
38	chr1:172405400-172412200	Weak transcription	Fetal Intestine Large	intestine
39	chr1:172405800-172411000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:172406400-172411800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:172407000-172411800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:172407200-172412200	Weak transcription	Fetal Brain Male	brain
43	chr1:172407400-172411000	Weak transcription	Fetal Brain Female	brain
44	chr1:172407400-172411000	Weak transcription	HSMM	muscle
45	chr1:172407400-172411800	Weak transcription	Fetal Lung	lung
46	chr1:172407600-172411000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:172407600-172411000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:172407800-172411000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:172407800-172412000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:172408000-172412000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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