Variant report

Variant	rs791801
Chromosome Location	chr1:176160057-176160058
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:176156157..176159032-chr1:176159209..176161354,2	K562	blood:
2	chr1:176159070..176161362-chr1:176173225..176174837,2	K562	blood:
3	chr1:176150222..176152761-chr1:176157686..176160252,3	K562	blood:
4	chr1:176156354..176160388-chr1:176161822..176166089,4	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10494499	0.83[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs10798449	0.83[ASN][1000 genomes]
rs10913150	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11801582	0.83[ASN][1000 genomes]
rs12239888	0.81[CHD][hapmap]
rs12403794	0.84[EUR][1000 genomes]
rs16849522	0.81[CHD][hapmap]
rs16849645	0.87[ASN][1000 genomes]
rs16849697	0.83[ASN][1000 genomes]
rs17351808	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs17351933	0.83[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17352072	0.91[EUR][1000 genomes]
rs17354252	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs1770643	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2039231	1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2039232	0.81[CHD][hapmap]
rs2136545	0.83[ASN][1000 genomes]
rs2481627	0.94[ASW][hapmap];0.91[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481634	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2481635	0.88[EUR][1000 genomes]
rs2481641	0.94[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap]
rs2481647	0.83[CEU][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2481651	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2481653	0.81[CHD][hapmap]
rs2481657	0.91[CEU][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502822	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502826	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502830	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2502832	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502834	0.94[ASW][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.85[ASN][1000 genomes]
rs2502835	0.85[ASN][1000 genomes]
rs2502836	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502841	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502842	0.91[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2502847	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2861630	0.83[CEU][hapmap];0.92[TSI][hapmap]
rs3845368	0.81[CHD][hapmap]
rs4129061	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4307526	0.90[AMR][1000 genomes]
rs4314844	0.90[AMR][1000 genomes]
rs4460596	0.83[CEU][hapmap]
rs4603086	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4650934	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4650938	0.83[ASN][1000 genomes]
rs4652143	1.00[CHD][hapmap]
rs4652148	0.81[CHD][hapmap]
rs471534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs533403	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553852	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56367284	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs580978	0.91[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59276566	0.83[ASN][1000 genomes]
rs60719126	0.86[EUR][1000 genomes]
rs611883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61821007	0.86[EUR][1000 genomes]
rs61821009	0.86[EUR][1000 genomes]
rs61821028	0.84[EUR][1000 genomes]
rs61821029	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61822662	0.91[EUR][1000 genomes]
rs6684747	0.86[AMR][1000 genomes]
rs6687043	0.88[ASW][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap]
rs6688211	0.85[YRI][hapmap]
rs6704509	0.91[CEU][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes]
rs704827	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs704832	0.91[CHD][hapmap];0.90[ASN][1000 genomes]
rs74127185	0.83[EUR][1000 genomes]
rs7524972	0.83[AMR][1000 genomes]
rs7545639	0.90[AMR][1000 genomes]
rs7554913	0.83[CEU][hapmap];0.92[TSI][hapmap]
rs791744	0.91[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs791795	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs791800	0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9783047	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs791801	PIGC	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176110600-176164000	Weak transcription	NHLF	lung
2	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
3	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
5	chr1:176137400-176173000	Weak transcription	Right Ventricle	heart
6	chr1:176140000-176168200	Weak transcription	Psoas Muscle	Psoas
7	chr1:176142800-176162200	Weak transcription	HepG2	liver
8	chr1:176143000-176165800	Weak transcription	Lung	lung
9	chr1:176144000-176172800	Weak transcription	HMEC	breast
10	chr1:176144400-176170800	Weak transcription	K562	blood
11	chr1:176144400-176173400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:176144600-176168600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:176144800-176164600	Weak transcription	NHDF-Ad	bronchial
14	chr1:176144800-176172800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:176145000-176173200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:176146000-176171400	Weak transcription	Left Ventricle	heart
17	chr1:176146000-176173000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:176147600-176161200	Weak transcription	HUVEC	blood vessel
19	chr1:176150600-176173000	Weak transcription	Hela-S3	cervix
20	chr1:176151800-176173000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:176152000-176168800	Weak transcription	Primary B cells from cord blood	blood
22	chr1:176152000-176168800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:176152000-176173000	Weak transcription	Thymus	Thymus
24	chr1:176153000-176161000	Weak transcription	Adipose Nuclei	Adipose
25	chr1:176153000-176161200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:176153000-176162400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:176153200-176165800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:176153200-176173000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:176153600-176161200	Weak transcription	Primary T cells from cord blood	blood
30	chr1:176153600-176169600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:176153600-176173000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:176153600-176173000	Weak transcription	HSMM	muscle
33	chr1:176153800-176166200	Weak transcription	Dnd41	blood
34	chr1:176154200-176160200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:176156000-176172600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:176156200-176162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:176157800-176167200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:176158000-176161600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:176158000-176161600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:176158000-176162200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:176158000-176166200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:176158400-176161200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:176158400-176161200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:176158400-176161400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:176159000-176162200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:176159400-176161800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:176159400-176164000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr1:176159600-176161000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:176159600-176161400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:176159600-176161600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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