Variant report

Variant	rs337189
Chromosome Location	chr1:220921156-220921157
allele	A/G
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	CEBPB	chr1:220921063-220921727	Hela-S3	cervix:	n/a	n/a
2	MYC	chr1:220921074-220922070	NB4	blood:	n/a	n/a
3	MAX	chr1:220921059-220922326	H1-hESC	embryonic stem cell:	n/a	chr1:220922195-220922205
4	POLR2A	chr1:220921131-220922327	Hela-S3	cervix:	n/a	n/a
5	TBP	chr1:220921073-220921854	Hela-S3	cervix:	n/a	n/a
6	E2F6	chr1:220920973-220922388	H1-hESC	embryonic stem cell:	n/a	chr1:220922158-220922167
7	CHD1	chr1:220921067-220922088	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:220921063-220922370	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF7L2	chr1:220921135-220922019	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:220920682-220922398	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr1:220921115-220922333	MCF-7	breast:	n/a	chr1:220922195-220922205
12	MAX	chr1:220921061-220922432	HCT-116	colon:	n/a	chr1:220922195-220922205
13	POLR2A	chr1:220921129-220922279	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr1:220921128-220922067	A549	lung:	n/a	n/a
15	SMARCC1	chr1:220920832-220921830	Hela-S3	cervix:	n/a	n/a
16	MXI1	chr1:220920620-220922531	SK-N-SH	brain:	n/a	chr1:220922203-220922212
17	GTF2F1	chr1:220920994-220922300	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr1:220921092-220922380	H1-hESC	embryonic stem cell:	n/a	chr1:220922195-220922205
19	MAX	chr1:220920957-220922392	A549	lung:	n/a	chr1:220922195-220922205
20	TAF1	chr1:220921083-220922392	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3A	chr1:220921110-220922361	H1-hESC	embryonic stem cell:	n/a	chr1:220921497-220921506
22	GTF2F1	chr1:220921135-220921810	Hela-S3	cervix:	n/a	n/a
23	MAX	chr1:220921144-220922179	H1-hESC	embryonic stem cell:	n/a	n/a
24	MYBL2	chr1:220921060-220921722	HepG2	liver:	n/a	n/a
25	HA-E2F1	chr1:220921138-220922467	MCF-7	breast:	n/a	chr1:220922158-220922167
26	MAX	chr1:220921087-220922364	ECC-1	luminal epithelium:	n/a	chr1:220922195-220922205
27	YY1	chr1:220921108-220922256	H1-hESC	embryonic stem cell:	n/a	chr1:220922166-220922177
28	MAX	chr1:220921105-220922290	HepG2	liver:	n/a	chr1:220922195-220922205
29	KAP1	chr1:220921032-220922534	HEK293	kidney:	n/a	n/a
30	YY1	chr1:220920838-220922413	H1-hESC	embryonic stem cell:	n/a	chr1:220922166-220922177
31	MAX	chr1:220920923-220922262	Hela-S3	cervix:	n/a	chr1:220922195-220922205
32	SMC3	chr1:220921100-220921825	Hela-S3	cervix:	n/a	n/a
33	HCFC1	chr1:220920817-220922779	Hela-S3	cervix:	n/a	n/a
34	TCF12	chr1:220921113-220921924	A549	lung:	n/a	n/a
35	MAX	chr1:220921079-220922344	A549	lung:	n/a	chr1:220922195-220922205
36	TEAD4	chr1:220921139-220921636	HepG2	liver:	n/a	n/a
37	MAX	chr1:220921087-220922155	NB4	blood:	n/a	n/a
38	E2F6	chr1:220921090-220922227	H1-hESC	embryonic stem cell:	n/a	chr1:220922158-220922167
39	POLR2A	chr1:220921092-220922040	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220862132..220866220-chr1:220920879..220923309,4	MCF-7	breast:
2	chr1:220920704..220923005-chr1:220929506..220932087,2	MCF-7	breast:
3	chr1:220920532..220923272-chr1:220926936..220929369,4	MCF-7	breast:
4	chr1:220915318..220916858-chr1:220919802..220921393,2	MCF-7	breast:
5	chr1:220920087..220922800-chr1:220958239..220960991,2	MCF-7	breast:

Variant related genes	Relation type
MARC2	TF binding region
ENSG00000117791	Chromatin interaction
ENSG00000162817	Chromatin interaction
ENSG00000186205	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10779415	0.93[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs10863562	0.93[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs11118597	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs12738691	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12758783	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs189231	0.89[ASW][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs234223	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2935225	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2994529	0.88[EUR][1000 genomes]
rs2994530	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3015251	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3015252	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs337147	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs337148	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs337150	0.81[EUR][1000 genomes]
rs337156	0.86[EUR][1000 genomes]
rs337157	0.82[MEX][hapmap]
rs337158	0.84[EUR][1000 genomes]
rs337159	0.86[EUR][1000 genomes]
rs337160	0.84[EUR][1000 genomes]
rs337161	0.84[EUR][1000 genomes]
rs337162	0.86[EUR][1000 genomes]
rs337164	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337187	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs337190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337191	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs365346	0.93[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs365398	0.84[EUR][1000 genomes]
rs365693	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3795536	0.93[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs381023	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs382959	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs386118	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs391315	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs393585	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs421736	0.84[EUR][1000 genomes]
rs425473	0.93[CEU][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes]
rs439130	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs443071	1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs443189	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6659246	0.84[TSI][hapmap]
rs6659604	0.89[EUR][1000 genomes]
rs774138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9430990	0.93[CEU][hapmap]

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	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv160470	chr1:220919015-220922779	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs337189	IARS2	cis	parietal	SCAN
rs337189	C1orf115	cis	multi-tissue	Pritchard
rs337189	C1orf115	Cis_1M	lymphoblastoid	RTeQTL
rs337189	MOSC2	cis	lymphoblastoid	seeQTL
rs337189	MOSC2	Cis_1M	lymphoblastoid	RTeQTL
rs337189	MOSC2	cis	cerebellum	SCAN
rs337189	C1orf115	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220915800-220921400	Weak transcription	Gastric	stomach
2	chr1:220916200-220921200	Weak transcription	Lung	lung
3	chr1:220918600-220921200	Weak transcription	Esophagus	oesophagus
4	chr1:220920200-220921200	Enhancers	Placenta	Placenta
5	chr1:220920400-220921400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
6	chr1:220920600-220921200	Flanking Active TSS	Fetal Heart	heart
7	chr1:220920600-220921400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
8	chr1:220920600-220921400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr1:220920600-220921600	Flanking Active TSS	Fetal Muscle Leg	muscle
10	chr1:220920600-220922600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:220920600-220922800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:220920800-220921200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
13	chr1:220920800-220921200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:220920800-220921200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr1:220920800-220921200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:220920800-220921200	Flanking Active TSS	Fetal Intestine Large	intestine
17	chr1:220920800-220921200	Bivalent Enhancer	Fetal Thymus	thymus
18	chr1:220920800-220921200	Flanking Active TSS	A549	lung
19	chr1:220920800-220921400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:220920800-220921400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:220920800-220921400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:220920800-220921400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:220920800-220921400	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr1:220920800-220921400	Flanking Active TSS	Liver	Liver
25	chr1:220920800-220921400	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr1:220920800-220921400	Flanking Active TSS	Fetal Brain Female	brain
27	chr1:220920800-220921400	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr1:220920800-220921400	Flanking Active TSS	Fetal Lung	lung
29	chr1:220920800-220921400	Flanking Active TSS	Fetal Muscle Trunk	muscle
30	chr1:220920800-220921400	Flanking Active TSS	Fetal Stomach	stomach
31	chr1:220920800-220921400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:220920800-220921400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr1:220920800-220921400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:220920800-220921400	Flanking Active TSS	Hela-S3	cervix
35	chr1:220920800-220921400	Flanking Bivalent TSS/Enh	HepG2	liver
36	chr1:220920800-220921600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr1:220920800-220921600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:220920800-220921600	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr1:220920800-220922400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr1:220920800-220922400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:220920800-220922600	Active TSS	Left Ventricle	heart
42	chr1:220920800-220922800	Active TSS	Fetal Kidney	kidney
43	chr1:220920800-220924000	Active TSS	Brain Anterior Caudate	brain
44	chr1:220920800-220924000	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:220920800-220924200	Active TSS	Brain Angular Gyrus	brain
46	chr1:220921000-220921200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:220921000-220921200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
48	chr1:220921000-220921200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:220921000-220921200	Enhancers	Brain Substantia Nigra	brain
50	chr1:220921000-220921200	Flanking Active TSS	Colonic Mucosa	Colon

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