Variant report

Variant	rs4883198
Chromosome Location	chr12:9070366-9070367
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9069248-9070637	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:9070340-9070390	H1-hESC	embryonic stem cell:	embryo
2	chr12:9070340-9070390	HRPEpiC	eye:	n/a
3	chr12:9070340-9070390	HEEpiC	esophagus:	n/a
4	chr12:9070340-9070390	HNPCEpiC	eye:	n/a
5	chr12:9070340-9070390	GM12891	blood:	n/a
6	chr12:9070340-9070390	GM19239	blood:	n/a
7	chr12:9070340-9070390	LNCaP	prostate:	n/a
8	chr12:9070340-9070390	GM12878	blood:	n/a
9	chr12:9070340-9070390	BJ	skin:	n/a
10	chr12:9070340-9070390	AG09309	skin:	n/a
11	chr12:9070340-9070390	PFSK-1	brain:	n/a
12	chr12:9070340-9070390	AG04450	lung:	fetal
13	chr12:9070340-9070390	GM06990	blood:	n/a
14	chr12:9070340-9070390	AG04449	skin:	fetal
15	chr12:9070340-9070390	HCF	heart:	n/a
16	chr12:9070340-9070390	NHDF-neo	bronchial:	n/a
17	chr12:9070340-9070390	HepG2	liver:	n/a
18	chr12:9070340-9070390	NT2-D1	testis:	n/a
19	chr12:9070340-9070390	SK-N-SH	brain:	n/a
20	chr12:9070340-9070390	SAEC	small airway:	n/a
21	chr12:9070340-9070390	RPTEC	kidney:	n/a
22	chr12:9070340-9070390	HIPEpiC	eye:	n/a
23	chr12:9070340-9070390	K562	blood:	n/a
24	chr12:9070340-9070390	ovcar-3	ovarian:	n/a
25	chr12:9070340-9070390	HPAEpiC	pulmonary alveolar:	n/a
26	chr12:9070340-9070390	Hela-S3	cervix:	n/a
27	chr12:9070340-9070390	PANC-1	pancreas:	n/a
28	chr12:9070340-9070390	Jurkat	blood:	n/a
29	chr12:9070340-9070390	AG09319	gingival:	n/a
30	chr12:9070340-9070390	Caco-2	colon:	n/a
31	chr12:9070340-9070390	NHBE	bronchial:	n/a
32	chr12:9070340-9070390	NB4	blood:	n/a
33	chr12:9070340-9070390	CMK	blood:	n/a
34	chr12:9070340-9070390	HAEpiC	amniotic membrane:	n/a
35	chr12:9070340-9070390	SK-N-SH_RA	brain:	n/a
36	chr12:9070340-9070390	Hepatocyte	liver:	n/a
37	chr12:9070340-9070390	NH-A	brain:	n/a
38	chr12:9070340-9070390	AG10803	skin:	n/a
39	chr12:9070340-9070390	MCF-7	breast:	n/a
40	chr12:9070340-9070390	IMR90	lung:	fetal
41	chr12:9070340-9070390	A549	lung:	n/a
42	chr12:9070340-9070390	HCPEpiC	choroid plexus:	n/a
43	chr12:9070340-9070390	MCF10A-Er-Src	breast:	n/a
44	chr12:9070340-9070390	HEK293	kidney:	embryo
45	chr12:9070340-9070390	HCM	heart:	n/a
46	chr12:9070340-9070390	ECC-1	luminal epithelium:	n/a
47	chr12:9070340-9070390	SK-N-MC	brain:	n/a
48	chr12:9070340-9070390	HCT-116	colon:	n/a
49	chr12:9070340-9070390	ProgFib	skin:	n/a
50	chr12:9070340-9070390	HMEC	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9066826..9070397-chr12:9099293..9102558,3	K562	blood:

No data

Variant related genes	Relation type
PHC1	TF binding region
PHC1	CpG island
ENSG00000003056	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10771204	0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10771216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047996	0.91[ASN][1000 genomes]
rs11048060	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805729	0.91[CEU][hapmap]
rs1805738	0.90[CEU][hapmap]
rs1805740	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805741	0.95[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1805762	0.85[JPT][hapmap]
rs1805776	0.89[CEU][hapmap]
rs1805778	0.93[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.91[ASN][1000 genomes]
rs3026261	0.90[CEU][hapmap]
rs3809218	0.93[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4882966	0.87[ASN][1000 genomes]
rs4882967	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4882968	0.88[ASN][1000 genomes]
rs4882969	0.87[ASN][1000 genomes]
rs4883197	0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4883199	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4883200	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297194	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7309772	0.91[ASN][1000 genomes]
rs7312166	0.85[ASN][1000 genomes]
rs7312676	0.84[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4883198	PHC1	cis	Artery Tibial	GTEx
rs4883198	PHC1	cis	Artery Aorta	GTEx
rs4883198	M6PR	cis	multi-tissue	Pritchard
rs4883198	PHC1	cis	Adipose Subcutaneous	GTEx
rs4883198	PHC1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9068200-9070400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:9068200-9070400	Enhancers	K562	blood
3	chr12:9068200-9070800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
4	chr12:9068200-9071000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:9068200-9071000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:9068200-9071200	Weak transcription	Fetal Intestine Large	intestine
7	chr12:9068200-9072000	Weak transcription	Left Ventricle	heart
8	chr12:9068200-9072200	Weak transcription	Fetal Intestine Small	intestine
9	chr12:9068200-9072400	Weak transcription	Aorta	Aorta
10	chr12:9068200-9072400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:9068200-9074000	Weak transcription	Liver	Liver
12	chr12:9068200-9074000	Weak transcription	Spleen	Spleen
13	chr12:9068200-9074800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:9068200-9075000	Weak transcription	Pancreas	Pancrea
15	chr12:9068200-9079000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:9068200-9084000	Weak transcription	Esophagus	oesophagus
17	chr12:9068200-9086400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:9068200-9088800	Weak transcription	Gastric	stomach
19	chr12:9068200-9091400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:9068200-9094200	Weak transcription	Colonic Mucosa	Colon
21	chr12:9068200-9094200	Weak transcription	Lung	lung
22	chr12:9068200-9094200	Weak transcription	Psoas Muscle	Psoas
23	chr12:9068200-9094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:9068200-9094200	Weak transcription	Small Intestine	intestine
25	chr12:9068200-9100000	Weak transcription	Stomach Mucosa	stomach
26	chr12:9068400-9070400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:9068400-9070600	Weak transcription	Placenta	Placenta
28	chr12:9068400-9070600	Weak transcription	Fetal Thymus	thymus
29	chr12:9068400-9070600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:9068400-9071000	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:9068400-9071200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:9068400-9071200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:9068400-9071400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:9068400-9072200	Weak transcription	NHEK	skin
35	chr12:9068400-9072400	Weak transcription	Adipose Nuclei	Adipose
36	chr12:9068400-9072400	Weak transcription	Right Ventricle	heart
37	chr12:9068400-9073600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:9068400-9073600	Weak transcription	HMEC	breast
39	chr12:9068400-9075000	Weak transcription	HSMMtube	muscle
40	chr12:9068400-9075400	Weak transcription	A549	lung
41	chr12:9068600-9071000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr12:9068600-9071000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:9068600-9071000	Weak transcription	Fetal Stomach	stomach
44	chr12:9068600-9071000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:9068600-9071200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:9068600-9071200	Weak transcription	Primary B cells from cord blood	blood
47	chr12:9068600-9071200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:9068600-9071200	Weak transcription	HSMM	muscle
49	chr12:9068600-9072000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:9068600-9073400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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