Variant report

Variant	rs57668887
Chromosome Location	chr1:172327399-172327400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:172221315..172226024-chr1:172325981..172331432,5	MCF-7	breast:
2	chr1:172313803..172316128-chr1:172326731..172328991,2	MCF-7	breast:
3	chr1:172293750..172296257-chr1:172325539..172327779,3	MCF-7	breast:
4	chr1:172291112..172293715-chr1:172326566..172328931,2	MCF-7	breast:
5	chr1:172147006..172149581-chr1:172326946..172329408,2	MCF-7	breast:
6	chr1:172057858..172060800-chr1:172327369..172328971,2	MCF-7	breast:
7	chr1:171972033..171974516-chr1:172324931..172327450,2	MCF-7	breast:
8	chr1:172326973..172328918-chr1:172367040..172369212,2	MCF-7	breast:
9	chr1:172327243..172328745-chr1:172418219..172419831,2	MCF-7	breast:
10	chr1:172319507..172323495-chr1:172324646..172327530,4	MCF-7	breast:
11	chr1:172327222..172329054-chr1:172342258..172344982,2	MCF-7	breast:
12	chr1:172324502..172327438-chr1:172328565..172330761,2	K562	blood:

No data

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1011731	0.81[ASN][1000 genomes]
rs1023479	0.80[ASN][1000 genomes]
rs10797996	0.81[ASN][1000 genomes]
rs10911654	0.80[ASN][1000 genomes]
rs12404665	0.81[ASN][1000 genomes]
rs1894633	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001129	0.82[ASN][1000 genomes]
rs2213732	0.81[ASN][1000 genomes]
rs2227200	0.82[ASN][1000 genomes]
rs2269612	0.81[ASN][1000 genomes]
rs2301453	0.81[ASN][1000 genomes]
rs3213564	0.80[ASN][1000 genomes]
rs34945663	0.81[ASN][1000 genomes]
rs4916251	0.80[ASN][1000 genomes]
rs4916252	0.81[ASN][1000 genomes]
rs6697844	0.96[ASN][1000 genomes]
rs714515	0.81[ASN][1000 genomes]
rs73046851	0.96[ASN][1000 genomes]
rs7534393	0.96[ASN][1000 genomes]
rs9425291	0.96[ASN][1000 genomes]
rs9425568	0.96[ASN][1000 genomes]
rs9425573	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425575	0.96[ASN][1000 genomes]
rs9425586	0.80[ASN][1000 genomes]
rs9425587	0.81[ASN][1000 genomes]
rs9425589	0.81[ASN][1000 genomes]
rs979935	0.96[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	nsv3543	chr1:172323563-172334586	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57668887	PIGC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172320800-172332800	Enhancers	Fetal Intestine Small	intestine
2	chr1:172321200-172329600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:172322400-172327600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:172322400-172329600	Weak transcription	Gastric	stomach
5	chr1:172322400-172331000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:172322600-172327800	Weak transcription	Psoas Muscle	Psoas
7	chr1:172322600-172328000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:172323000-172333000	Enhancers	Fetal Intestine Large	intestine
9	chr1:172323600-172328200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:172325200-172327600	Enhancers	HMEC	breast
11	chr1:172325200-172328000	Flanking Active TSS	A549	lung
12	chr1:172325600-172327800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:172325600-172331000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:172325800-172327600	Enhancers	NHLF	lung
15	chr1:172325800-172328000	Enhancers	HSMMtube	muscle
16	chr1:172325800-172331400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:172326000-172327600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:172326000-172327800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:172326200-172327800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr1:172326200-172330800	Enhancers	Stomach Mucosa	stomach
21	chr1:172326400-172327600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:172326400-172327600	Flanking Active TSS	GM12878-XiMat	blood
23	chr1:172326400-172328600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:172326400-172328600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:172326400-172329800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:172326400-172330200	Enhancers	HSMM	muscle
27	chr1:172326400-172330400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:172326400-172331200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:172326600-172327600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:172326600-172330600	Enhancers	Brain Cingulate Gyrus	brain
31	chr1:172326600-172332200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:172326800-172327400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:172326800-172327400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:172326800-172327600	Enhancers	Primary T cells from cord blood	blood
35	chr1:172326800-172327800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:172326800-172327800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:172326800-172327800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:172326800-172327800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:172326800-172329600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:172326800-172329800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr1:172326800-172330400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:172326800-172330600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:172327000-172327400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:172327000-172327400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:172327000-172327400	Enhancers	Brain Hippocampus Middle	brain
46	chr1:172327000-172327400	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr1:172327000-172327400	Flanking Active TSS	Fetal Kidney	kidney
48	chr1:172327000-172327400	Enhancers	Stomach Smooth Muscle	stomach
49	chr1:172327000-172327600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:172327000-172327600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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