Variant report

Variant	rs3027012
Chromosome Location	chr1:159174123-159174124
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	MAX	chr1:159173884-159174430	K562	blood:	n/a	chr1:159174159-159174166 chr1:159174156-159174165 chr1:159174157-159174167
2	GATA1	chr1:159173489-159175322	PBDE	blood:	n/a	chr1:159174313-159174323 chr1:159174315-159174332 chr1:159174671-159174692 chr1:159174314-159174323 chr1:159174679-159174696 chr1:159174678-159174685 chr1:159174314-159174321 chr1:159174678-159174685 chr1:159174312-159174325 chr1:159174678-159174685
3	BHLHE40	chr1:159173666-159174771	K562	blood:	n/a	n/a
4	MYC	chr1:159173959-159174836	K562	blood:	n/a	chr1:159174159-159174166 chr1:159174156-159174165 chr1:159174157-159174167
5	JUND	chr1:159173467-159174386	K562	blood:	n/a	n/a
6	POLR2A	chr1:159173266-159177005	PBDE	blood:	n/a	n/a
7	NR3C1	chr1:159173945-159174255	A549	lung:	n/a	n/a
8	EGR1	chr1:159173885-159174238	K562	blood:	n/a	chr1:159174155-159174164 chr1:159174153-159174167 chr1:159174155-159174165 chr1:159174154-159174167 chr1:159174155-159174165
9	UBTF	chr1:159174103-159174861	K562	blood:	n/a	n/a
10	TBL1XR1	chr1:159173979-159174279	K562	blood:	n/a	n/a
11	MAX	chr1:159173989-159174230	K562	blood:	n/a	chr1:159174159-159174166 chr1:159174156-159174165 chr1:159174157-159174167
12	RCOR1	chr1:159174038-159174353	K562	blood:	n/a	n/a
13	TAL1	chr1:159173931-159174905	K562	blood:	n/a	chr1:159174677-159174685 chr1:159174678-159174696 chr1:159174314-159174332
14	ZBTB7A	chr1:159173979-159174133	K562	blood:	n/a	n/a
15	NR3C1	chr1:159173927-159174327	A549	lung:	n/a	n/a
16	CEBPB	chr1:159173905-159174163	K562	blood:	n/a	n/a
17	TBL1XR1	chr1:159174047-159174853	K562	blood:	n/a	n/a
18	MAZ	chr1:159173473-159175086	K562	blood:	n/a	chr1:159174159-159174166 chr1:159174156-159174165 chr1:159173637-159173647 chr1:159174157-159174167
19	UBTF	chr1:159173961-159174308	K562	blood:	n/a	n/a
20	EP300	chr1:159173530-159174850	K562	blood:	n/a	chr1:159173953-159173963 chr1:159173591-159173605
21	MAX	chr1:159173529-159174843	K562	blood:	n/a	chr1:159174159-159174166 chr1:159174156-159174165 chr1:159173637-159173647 chr1:159174157-159174167
22	RCOR1	chr1:159173996-159174844	K562	blood:	n/a	n/a
23	EGR1	chr1:159174057-159174216	K562	blood:	n/a	chr1:159174155-159174164 chr1:159174153-159174167 chr1:159174155-159174165 chr1:159174154-159174167 chr1:159174155-159174165
24	MYC	chr1:159173970-159174404	K562	blood:	n/a	chr1:159174159-159174166 chr1:159174156-159174165 chr1:159174157-159174167

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:159174076-159174126	NH-A	brain:	n/a
2	chr1:159174076-159174126	RPTEC	kidney:	n/a
3	chr1:159174076-159174126	AoSMC	blood vessel:	n/a
4	chr1:159174076-159174126	ovcar-3	ovarian:	n/a
5	chr1:159174076-159174126	A549	lung:	n/a
6	chr1:159174076-159174126	PFSK-1	brain:	n/a
7	chr1:159174076-159174126	HRE	kidney:	n/a
8	chr1:159174076-159174126	IMR90	lung:	fetal
9	chr1:159174076-159174126	AG04450	lung:	fetal
10	chr1:159174076-159174126	ProgFib	skin:	n/a
11	chr1:159174076-159174126	HCT-116	colon:	n/a
12	chr1:159174076-159174126	LNCaP	prostate:	n/a
13	chr1:159174076-159174126	T-47D	breast:	n/a
14	chr1:159174076-159174126	GM12892	blood:	n/a
15	chr1:159174076-159174126	HNPCEpiC	eye:	n/a
16	chr1:159174076-159174126	HCM	heart:	n/a
17	chr1:159174076-159174126	Hela-S3	cervix:	n/a
18	chr1:159174076-159174126	HepG2	liver:	n/a
19	chr1:159174076-159174126	BE2_C	brain:	n/a
20	chr1:159174076-159174126	HRPEpiC	eye:	n/a
21	chr1:159174076-159174126	SK-N-SH	brain:	n/a
22	chr1:159174076-159174126	NHDF-neo	bronchial:	n/a
23	chr1:159174076-159174126	HCPEpiC	choroid plexus:	n/a
24	chr1:159174076-159174126	MCF10A-Er-Src	breast:	n/a
25	chr1:159174076-159174126	HUVEC	blood vessel:	n/a
26	chr1:159174076-159174126	PANC-1	pancreas:	n/a
27	chr1:159174076-159174126	SKMC	muscle:	n/a
28	chr1:159174076-159174126	AG04449	skin:	fetal
29	chr1:159174076-159174126	HMEC	breast:	n/a
30	chr1:159174076-159174126	NT2-D1	testis:	n/a
31	chr1:159174076-159174126	SK-N-MC	brain:	n/a
32	chr1:159174076-159174126	SAEC	small airway:	n/a
33	chr1:159174076-159174126	PrEC	prostate:	n/a
34	chr1:159174076-159174126	HEEpiC	esophagus:	n/a
35	chr1:159174076-159174126	K562	blood:	n/a
36	chr1:159174076-159174126	HEK293	kidney:	embryo
37	chr1:159174076-159174126	AG09309	skin:	n/a
38	chr1:159174076-159174126	Jurkat	blood:	n/a
39	chr1:159174076-159174126	H1-hESC	embryonic stem cell:	embryo
40	chr1:159174076-159174126	Hepatocyte	liver:	n/a
41	chr1:159174076-159174126	AG10803	skin:	n/a
42	chr1:159174076-159174126	GM06990	blood:	n/a
43	chr1:159174076-159174126	AG09319	gingival:	n/a
44	chr1:159174076-159174126	Caco-2	colon:	n/a
45	chr1:159174076-159174126	GM12878	blood:	n/a
46	chr1:159174076-159174126	HAEpiC	amniotic membrane:	n/a
47	chr1:159174076-159174126	U87	brain:	n/a
48	chr1:159174076-159174126	HCF	heart:	n/a
49	chr1:159174076-159174126	HIPEpiC	eye:	n/a
50	chr1:159174076-159174126	SK-N-SH_RA	brain:	n/a

Variant related genes	Relation type
ENSG00000225670	TF binding region
DARC	TF binding region
DARC	CpG island
ENSG00000225670	CpG island

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10489849	0.91[ASN][1000 genomes]
rs11265150	0.91[ASN][1000 genomes]
rs12063098	0.83[ASN][1000 genomes]
rs12095174	0.91[ASN][1000 genomes]
rs12410844	0.83[ASN][1000 genomes]
rs2814778	1.00[LWK][hapmap]
rs3027008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3027034	1.00[ASN][1000 genomes]
rs3027076	0.91[ASN][1000 genomes]
rs34029634	0.83[ASN][1000 genomes]
rs34217855	0.83[ASN][1000 genomes]
rs34683667	0.91[ASN][1000 genomes]
rs35113846	0.91[ASN][1000 genomes]
rs35333710	1.00[ASN][1000 genomes]
rs35405068	0.91[ASN][1000 genomes]
rs35610895	0.91[ASN][1000 genomes]
rs6676002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687584	0.91[ASN][1000 genomes]
rs6687589	0.91[ASN][1000 genomes]
rs7533790	0.83[ASN][1000 genomes]
rs862990	0.88[CEU][hapmap]
rs862991	0.83[CEU][hapmap]
rs862996	0.88[CEU][hapmap]
rs862999	0.88[CEU][hapmap]
rs863002	1.00[LWK][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3027012	PIGM	cis	cerebellum	SCAN
rs3027012	KCNJ9	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159158800-159177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:159158800-159177800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:159158800-159188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:159168000-159177600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:159168400-159177600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:159170400-159174200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:159170400-159177800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:159170800-159174400	Enhancers	Lung	lung
9	chr1:159170800-159177600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:159171400-159174800	Weak transcription	Esophagus	oesophagus
11	chr1:159171800-159174800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:159171800-159176000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:159172200-159174400	Enhancers	Spleen	Spleen
14	chr1:159172200-159175800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:159172600-159177200	Weak transcription	Brain Germinal Matrix	brain
16	chr1:159173000-159176400	Enhancers	GM12878-XiMat	blood
17	chr1:159173200-159174600	Weak transcription	Fetal Brain Female	brain
18	chr1:159173400-159174800	Flanking Active TSS	K562	blood
19	chr1:159173400-159176200	Enhancers	Placenta	Placenta
20	chr1:159173600-159174200	Enhancers	Brain Anterior Caudate	brain
21	chr1:159173600-159175800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:159173800-159175000	Enhancers	Fetal Brain Male	brain
23	chr1:159174000-159174200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:159174000-159174600	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:159174000-159175200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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