Variant report

Variant	rs4603880
Chromosome Location	chr22:31744721-31744722
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	POLR2A	chr22:31744579-31745185	HepG2	liver:	n/a	n/a
2	POLR2A	chr22:31744707-31745102	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr22:31744529-31745435	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31738670..31747056-chr22:31790500..31799012,36	MCF-7	breast:
2	chr22:31737798..31746418-chr22:31793074..31801662,34	MCF-7	breast:
3	chr10:74033244..74035559-chr22:31742440..31745127,2	MCF-7	breast:
4	chr22:31696471..31699232-chr22:31743755..31746050,2	MCF-7	breast:

Variant related genes	Relation type
PATZ1	TF binding region
ENSG00000168209	Chromatin interaction
ENSG00000185721	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1034589	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs12152166	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13054220	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056485	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs131205	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13158	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs1858821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1968023	1.00[LWK][hapmap]
rs2040533	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073857	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078803	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2079431	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2106294	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228619	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273249	0.95[CEU][hapmap]
rs2273251	0.95[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283881	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413033	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2413034	0.82[EUR][1000 genomes]
rs2413035	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413045	1.00[MKK][hapmap]
rs2413046	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413047	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413049	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899164	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs34545960	0.85[EUR][1000 genomes]
rs4141404	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4299418	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820042	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820043	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820951	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4820963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749224	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs5749229	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749243	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749265	0.86[EUR][1000 genomes]
rs5749267	0.85[EUR][1000 genomes]
rs5749268	0.85[EUR][1000 genomes]
rs5749270	0.85[EUR][1000 genomes]
rs5749286	0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs5749298	0.83[GIH][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap]
rs5753500	0.81[EUR][1000 genomes]
rs5753507	0.80[EUR][1000 genomes]
rs5753521	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753597	0.86[EUR][1000 genomes]
rs5753601	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs5753609	0.90[CEU][hapmap];0.88[TSI][hapmap]
rs5753610	0.85[EUR][1000 genomes]
rs5753612	0.84[EUR][1000 genomes]
rs5753613	0.84[EUR][1000 genomes]
rs5753632	0.95[CEU][hapmap];0.88[TSI][hapmap]
rs5753639	0.95[CEU][hapmap];0.88[TSI][hapmap]
rs5753659	0.87[TSI][hapmap]
rs5753669	0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs5753671	0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs5994394	0.85[EUR][1000 genomes]
rs5997893	0.85[MEX][hapmap]
rs5997902	0.83[EUR][1000 genomes]
rs5997912	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs5997933	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997939	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997949	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71324184	0.93[EUR][1000 genomes]
rs714909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs715510	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285619	0.95[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs7287267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7293171	0.85[EUR][1000 genomes]
rs737684	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs738657	0.95[CEU][hapmap]
rs8135344	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8135347	0.83[EUR][1000 genomes]
rs8135417	0.85[MEX][hapmap]
rs8138596	0.92[EUR][1000 genomes]
rs8141150	0.85[EUR][1000 genomes]
rs9606830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606839	0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs9606843	0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs9606848	0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs9609254	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609257	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9609264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609266	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609267	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609268	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609276	0.84[EUR][1000 genomes]
rs9609277	0.85[EUR][1000 genomes]
rs9609296	0.83[GIH][hapmap];0.91[TSI][hapmap]
rs9609297	0.84[TSI][hapmap]
rs9609304	0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs9621235	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv3333136	chr22:31704947-31758417	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1816779	chr22:31743711-31797094	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4603880	SFI1	cis	cerebellum	SCAN
rs4603880	MN1	cis	parietal	SCAN
rs4603880	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs4603880	SFI1	cis	Thyroid	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31744000-31744800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr22:31744000-31745000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:31744000-31745000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:31744000-31745000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr22:31744000-31745800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr22:31744000-31746000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr22:31744000-31746000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr22:31744000-31746200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr22:31744000-31746200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:31744000-31746200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:31744000-31746200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr22:31744000-31746200	Weak transcription	A549	lung
13	chr22:31744000-31746600	Weak transcription	Fetal Lung	lung
14	chr22:31744000-31762200	Weak transcription	Right Atrium	heart
15	chr22:31744200-31744800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr22:31744200-31745000	Weak transcription	Colon Smooth Muscle	Colon
17	chr22:31744200-31745000	Enhancers	Dnd41	blood
18	chr22:31744200-31745000	Enhancers	HepG2	liver
19	chr22:31744200-31745800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr22:31744200-31746000	Weak transcription	HSMMtube	muscle
21	chr22:31744200-31746400	Weak transcription	Liver	Liver
22	chr22:31744200-31746400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr22:31744200-31746400	Weak transcription	Fetal Heart	heart
24	chr22:31744200-31746400	Weak transcription	Fetal Stomach	stomach
25	chr22:31744200-31746600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr22:31744200-31748400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr22:31744200-31750400	Weak transcription	Spleen	Spleen
28	chr22:31744400-31744800	Weak transcription	Pancreas	Pancrea
29	chr22:31744600-31745000	Enhancers	Colonic Mucosa	Colon

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