Variant report

Variant	rs880098
Chromosome Location	chr1:71520103-71520104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:71519303-71520801	K562	blood:	n/a	n/a
2	POLR2A	chr1:71519776-71520506	HCT-116	colon:	n/a	n/a
3	POLR2A	chr1:71519976-71520420	A549	lung:	n/a	n/a
4	BCL3	chr1:71519880-71520371	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:71519697-71521224	U87	brain:	n/a	n/a
6	POLR2A	chr1:71518549-71523144	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:71519204-71521209	SK-N-MC	brain:	n/a	n/a
8	CCNT2	chr1:71520018-71520518	K562	blood:	n/a	chr1:71520339-71520348
9	POLR2A	chr1:71518581-71521507	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:71519828-71521545	PANC-1	pancreas:	n/a	n/a
11	BCL3	chr1:71519995-71520422	A549	lung:	n/a	n/a
12	POLR2A	chr1:71518735-71520733	GM12878	blood:	n/a	n/a
13	BCLAF1	chr1:71520077-71520541	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:71519228-71521083	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:71519938-71520963	K562	blood:	n/a	n/a
16	POLR2A	chr1:71519954-71520682	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:71519316-71521045	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:71515710-71520875	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:71518500-71525451	GM12878	blood:	n/a	n/a
20	MTA3	chr1:71519193-71521241	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:71519929-71520363	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:71518529-71521641	GM12891	blood:	n/a	n/a
23	POLR2A	chr1:71517482-71520991	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:71519230-71520750	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr1:71519864-71520690	K562	blood:	n/a	n/a
26	POLR2A	chr1:71519266-71521648	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:71519322-71521551	K562	blood:	n/a	n/a
28	BCL3	chr1:71520059-71520490	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:71518564-71521493	GM12892	blood:	n/a	n/a
30	POLR2A	chr1:71519955-71520835	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:71519186-71521259	A549	lung:	n/a	n/a
32	POLR2A	chr1:71519288-71520752	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:71519332-71520985	PBDE	blood:	n/a	n/a
34	POLR2A	chr1:71519459-71520964	NB4	blood:	n/a	n/a
35	POLR2A	chr1:71519696-71521224	U87	brain:	n/a	n/a
36	NFATC1	chr1:71518743-71521240	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:71519592-71521505	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr1:71519912-71520456	A549	lung:	n/a	n/a
39	PML	chr1:71519168-71520628	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:71518050-71545780	K562	blood:	n/a	n/a
41	POLR2A	chr1:71519824-71520621	GM12892	blood:	n/a	n/a
42	POLR2A	chr1:71519304-71521335	HL-60	blood:	n/a	n/a
43	POLR2A	chr1:71519541-71521146	SK-N-SH	brain:	n/a	n/a
44	STAT5A	chr1:71520071-71520408	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:71519805-71520289	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:71519840-71521071	GM12891	blood:	n/a	n/a
47	POLR2A	chr1:71518523-71521648	SK-N-MC	brain:	n/a	n/a
48	RFX5	chr1:71520023-71520153	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:71519303-71520878	GM15510	blood:	n/a	n/a
50	POLR2A	chr1:71519796-71520964	MCF-7	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:71374929..71377417-chr1:71518030..71520956,2	K562	blood:
2	chr1:71389776..71391612-chr1:71519550..71521085,2	K562	blood:
3	chr1:70975411..70978050-chr1:71517707..71520694,2	K562	blood:

No data

Variant related genes	Relation type
ZRANB2-AS1	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1009311	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1022527	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1022529	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10399704	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10399705	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10399706	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10399797	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10493481	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11209736	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11209739	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11209740	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11209743	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11209745	0.84[ASN][1000 genomes]
rs11209747	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209756	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1138177	0.84[ASN][1000 genomes]
rs12084460	0.81[ASN][1000 genomes]
rs12118599	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12119958	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12120041	0.86[AMR][1000 genomes]
rs12134962	0.85[AMR][1000 genomes]
rs12139565	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12139719	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12139935	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12729268	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12739047	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12739685	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12748649	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12756951	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12757161	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1418449	0.85[ASN][1000 genomes]
rs1573061	0.81[ASN][1000 genomes]
rs1832900	0.86[ASN][1000 genomes]
rs1954285	0.81[ASN][1000 genomes]
rs2066371	0.81[ASN][1000 genomes]
rs2066373	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2143157	0.84[AMR][1000 genomes]
rs2179412	0.84[AMR][1000 genomes]
rs2268054	0.83[AFR][1000 genomes]
rs2300178	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2639329	0.81[ASN][1000 genomes]
rs2639335	0.81[ASN][1000 genomes]
rs2639338	0.81[ASN][1000 genomes]
rs2796187	0.81[ASN][1000 genomes]
rs2796188	0.81[ASN][1000 genomes]
rs2796189	0.81[ASN][1000 genomes]
rs2796190	0.81[ASN][1000 genomes]
rs2796196	0.88[ASN][1000 genomes]
rs2796201	0.81[ASN][1000 genomes]
rs2796202	0.81[ASN][1000 genomes]
rs2817864	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2817869	1.00[ASN][1000 genomes]
rs2901523	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4128461	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4272572	0.96[ASN][1000 genomes]
rs4367753	0.88[ASN][1000 genomes]
rs4397614	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4425938	0.81[ASN][1000 genomes]
rs4520371	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4650099	0.97[EUR][1000 genomes]
rs4650100	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs66461782	0.84[ASN][1000 genomes]
rs6680193	0.96[ASN][1000 genomes]
rs7411	1.00[ASN][1000 genomes]
rs7516464	0.83[ASN][1000 genomes]
rs7525785	0.84[AMR][1000 genomes]
rs7556111	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8179367	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8179390	0.88[AMR][1000 genomes]
rs8179408	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs952337	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases
2	nsv945995	chr1:71517111-71520224	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs880098	PTGER3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71513600-71533600	Weak transcription	Lung	lung
2	chr1:71514000-71525000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:71514000-71527400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:71514000-71530600	Weak transcription	Ovary	ovary
5	chr1:71514000-71533600	Weak transcription	Pancreas	Pancrea
6	chr1:71514000-71533600	Weak transcription	Right Ventricle	heart
7	chr1:71514200-71524200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:71514200-71533600	Weak transcription	Spleen	Spleen
9	chr1:71514400-71524400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:71515800-71521400	Weak transcription	Adipose Nuclei	Adipose
11	chr1:71515800-71522400	Weak transcription	Liver	Liver
12	chr1:71515800-71522800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:71515800-71523200	Weak transcription	Dnd41	blood
14	chr1:71515800-71524600	Weak transcription	Fetal Brain Female	brain
15	chr1:71515800-71524800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:71515800-71525000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:71515800-71525200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:71515800-71526000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:71515800-71541000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:71516000-71520600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:71516000-71524400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:71516800-71522000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:71517000-71522000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:71517000-71522200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:71517000-71522800	Weak transcription	Fetal Thymus	thymus
26	chr1:71517000-71526000	Weak transcription	Thymus	Thymus
27	chr1:71517200-71522600	Weak transcription	Primary T cells from cord blood	blood
28	chr1:71517200-71523200	Weak transcription	K562	blood
29	chr1:71517400-71522000	Weak transcription	Primary B cells from cord blood	blood
30	chr1:71517600-71523000	Weak transcription	Osteobl	bone
31	chr1:71517600-71524400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:71517600-71525000	Weak transcription	NHDF-Ad	bronchial
33	chr1:71518000-71523400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:71518200-71522000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:71518200-71522000	Weak transcription	HMEC	breast
36	chr1:71518200-71523600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:71518200-71523800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:71518600-71520200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:71518600-71522000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:71518600-71523000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:71518800-71522200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:71518800-71523600	Weak transcription	Fetal Lung	lung
43	chr1:71518800-71524400	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:71519000-71522200	Weak transcription	GM12878-XiMat	blood
45	chr1:71519000-71522600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:71519000-71522600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr1:71519000-71523800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:71519000-71526200	Weak transcription	Brain Substantia Nigra	brain
49	chr1:71519000-71530200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:71519200-71523000	Weak transcription	A549	lung

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