Variant report

Variant	rs7517351
Chromosome Location	chr1:175917500-175917501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10158829	0.82[CHB][hapmap]
rs10436864	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494496	0.82[CHB][hapmap]
rs10737315	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10737316	1.00[CHB][hapmap]
rs10753111	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10798427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10798428	0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798431	1.00[CHB][hapmap]
rs10798432	0.85[CHB][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs10913109	0.88[AMR][1000 genomes]
rs1155229	0.92[ASN][1000 genomes]
rs11576471	0.82[ASN][1000 genomes]
rs11576862	0.86[EUR][1000 genomes]
rs11806468	0.82[CHB][hapmap]
rs12029090	0.84[YRI][hapmap]
rs12038027	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1357337	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];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522637	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs16849522	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs17351808	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs1770643	0.82[AMR][1000 genomes]
rs1831447	0.82[CHB][hapmap]
rs2039231	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs2039232	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs2481627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.81[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs2481634	0.81[AMR][1000 genomes]
rs2481641	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2481647	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2481651	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481653	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2481657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502824	1.00[CHB][hapmap]
rs2502826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502830	0.84[AMR][1000 genomes]
rs2502832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2502834	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs2502835	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs2502836	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2502841	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2502842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes]
rs2502847	0.81[AMR][1000 genomes]
rs2861629	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2861630	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs4129061	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4304533	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs4307526	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4314844	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4460596	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs4543747	1.00[CHB][hapmap]
rs4603086	0.82[AMR][1000 genomes]
rs4652143	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4652148	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs553852	0.81[AMR][1000 genomes]
rs56367284	0.81[AMR][1000 genomes]
rs60964243	0.86[EUR][1000 genomes]
rs61820953	0.86[EUR][1000 genomes]
rs61820960	0.84[EUR][1000 genomes]
rs61821029	0.81[AMR][1000 genomes]
rs61822767	0.84[EUR][1000 genomes]
rs6425367	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6425368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661828	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6680309	0.91[EUR][1000 genomes]
rs6684747	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6687043	0.82[ASW][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.90[ASN][1000 genomes]
rs6688211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[ASN][1000 genomes]
rs6704509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74127150	0.91[EUR][1000 genomes]
rs74127154	0.86[EUR][1000 genomes]
rs7522442	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7524972	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7536464	1.00[CHB][hapmap]
rs7537435	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537480	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7539247	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7543769	1.00[CHB][hapmap]
rs7545043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7545639	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7546538	0.85[ASN][1000 genomes]
rs7552181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7554913	0.91[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs9783047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7517351	PIGC	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175874400-175945600	Weak transcription	A549	lung
2	chr1:175880000-175937800	Weak transcription	HSMMtube	muscle
3	chr1:175881000-175924200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:175886400-175929400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:175887800-175929800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:175889200-175937800	Weak transcription	Osteobl	bone
7	chr1:175892400-175940600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:175893200-175943000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:175897000-175953000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:175897600-175953200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:175897800-175952400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:175898600-175953200	Weak transcription	Pancreas	Pancrea
13	chr1:175899200-175953200	Weak transcription	Esophagus	oesophagus
14	chr1:175901600-175940600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:175901800-175925800	Weak transcription	HUVEC	blood vessel
16	chr1:175902400-175917800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:175902800-175931800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:175903200-175924200	Weak transcription	Gastric	stomach
19	chr1:175903400-175951400	Weak transcription	K562	blood
20	chr1:175903600-175940800	Weak transcription	HMEC	breast
21	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
22	chr1:175904600-175953000	Weak transcription	Right Ventricle	heart
23	chr1:175905000-175946800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:175905400-175918800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:175905600-175918800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:175906000-175918200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:175906000-175930000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:175906200-175917600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:175906200-175919000	Weak transcription	Fetal Brain Male	brain
30	chr1:175906400-175920800	Weak transcription	HepG2	liver
31	chr1:175906400-175940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:175906400-175944800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:175906400-175952400	Weak transcription	Spleen	Spleen
34	chr1:175906400-175962600	Weak transcription	NH-A	brain
35	chr1:175906600-175921200	Weak transcription	Fetal Stomach	stomach
36	chr1:175906800-175921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:175906800-175952000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:175907400-175921200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:175907400-175950600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:175907800-175937400	Weak transcription	NHLF	lung
41	chr1:175907800-175940600	Weak transcription	Colonic Mucosa	Colon
42	chr1:175907800-175945400	Weak transcription	Small Intestine	intestine
43	chr1:175907800-175945600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:175908000-175920000	Weak transcription	Fetal Intestine Small	intestine
45	chr1:175908000-175959400	Weak transcription	NHEK	skin
46	chr1:175908200-175939400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:175908400-175919000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:175908600-175917800	Strong transcription	Primary B cells from cord blood	blood
49	chr1:175909400-175948000	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:175909600-175920600	Weak transcription	Fetal Muscle Trunk	muscle

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