Variant report

Variant	rs33984028
Chromosome Location	chr3:42622781-42622782
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	MXI1	chr3:42622689-42624175	Hela-S3	cervix:	n/a	n/a
2	UBTF	chr3:42622742-42624155	K562	blood:	n/a	n/a
3	EP300	chr3:42622357-42622921	GM12878	blood:	n/a	chr3:42622514-42622524
4	TBP	chr3:42622251-42624089	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr3:42622750-42624302	SK-N-SH	brain:	n/a	chr3:42622895-42622902
6	MYC	chr3:42622769-42624248	K562	blood:	n/a	n/a
7	MAZ	chr3:42622691-42624047	IMR90	lung:	n/a	n/a
8	IRF1	chr3:42622184-42622929	K562	blood:	n/a	chr3:42622625-42622639
9	MYC	chr3:42622600-42624159	K562	blood:	n/a	n/a
10	MXI1	chr3:42622487-42624614	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:42622445-42623971	MCF10A-Er-Src	breast:	n/a	n/a
12	MXI1	chr3:42622717-42624505	IMR90	lung:	n/a	n/a
13	NR2F2	chr3:42622769-42624376	K562	blood:	n/a	n/a
14	NRF1	chr3:42622739-42624208	SK-N-SH	brain:	n/a	chr3:42623459-42623473 chr3:42623438-42623449 chr3:42623464-42623473 chr3:42623462-42623473 chr3:42623462-42623473 chr3:42623318-42623327
15	JUN	chr3:42621793-42625488	K562	blood:	n/a	chr3:42622871-42622885
16	POLR2A	chr3:42622750-42624103	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:42622731-42624191	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr3:42622759-42623043	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42622324..42624855-chr3:42675398..42677179,2	K562	blood:
2	chr3:42622045..42625365-chr3:42627615..42632564,8	MCF-7	breast:
3	chr3:42622691..42623310-chr7:45017186..45017698,2	Hela-S3	cervix:
4	chr10:90750277..90752970-chr3:42621806..42623827,2	MCF-7	breast:
5	chr3:42540384..42544045-chr3:42620631..42622853,3	K562	blood:
6	chr3:42620803..42625287-chr3:42629964..42635186,7	MCF-7	breast:
7	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
8	chr3:42621283..42625330-chr3:42639303..42643596,7	MCF-7	breast:
9	chr3:42622499..42623320-chr9:91933312..91933841,2	Hela-S3	cervix:
10	chr3:42622208..42623993-chr3:42640628..42642693,2	MCF-7	breast:

Variant related genes	Relation type
SS18L2	TF binding region
ENSG00000114812	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000187742	Chromatin interaction
ENSG00000026103	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000107796	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1062051	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13085695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13089845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13090902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13093680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13095447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17074602	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17074662	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17074664	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17074669	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17074673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17074674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17074680	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17074693	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2241542	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2284303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2284304	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300058	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2302352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33969824	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34683820	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34687113	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34762478	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34801786	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34852409	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34977988	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35676838	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36033201	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774402	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774404	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821836	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs3846058	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3846059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3856737	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3886782	0.87[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs56797870	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57259216	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58868911	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59914338	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60232916	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60348477	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66786953	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67059259	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67165547	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67533173	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.88[ASN][1000 genomes]
rs6778982	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6782164	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6790204	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6793186	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6795296	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6797491	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68071013	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72864072	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7616701	0.85[TSI][hapmap]
rs7617403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7617736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs33984028	CCR1	cis	cerebellum	SCAN
rs33984028	SNORA62	cis	parietal	SCAN
rs33984028	C3orf39	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42603000-42622800	Weak transcription	Colonic Mucosa	Colon
2	chr3:42604200-42622800	Weak transcription	Psoas Muscle	Psoas
3	chr3:42604200-42623000	Weak transcription	Esophagus	oesophagus
4	chr3:42607800-42622800	Weak transcription	Pancreas	Pancrea
5	chr3:42608000-42623000	Weak transcription	Gastric	stomach
6	chr3:42608600-42622800	Weak transcription	Aorta	Aorta
7	chr3:42609000-42622800	Weak transcription	HSMMtube	muscle
8	chr3:42609000-42623000	Weak transcription	Spleen	Spleen
9	chr3:42609600-42623000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:42610600-42623000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:42611400-42622800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:42611600-42622800	Weak transcription	Ovary	ovary
13	chr3:42614200-42622800	Weak transcription	Left Ventricle	heart
14	chr3:42615000-42623000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:42615000-42623000	Weak transcription	Lung	lung
16	chr3:42616600-42622800	Weak transcription	Placenta	Placenta
17	chr3:42617400-42622800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:42617400-42622800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:42617400-42622800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:42617400-42622800	Weak transcription	Fetal Intestine Small	intestine
21	chr3:42617400-42622800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:42621000-42622800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:42621600-42622800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:42621600-42622800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr3:42621600-42622800	Enhancers	Adipose Nuclei	Adipose
26	chr3:42621600-42622800	Enhancers	Stomach Mucosa	stomach
27	chr3:42621800-42622800	Enhancers	Primary B cells from cord blood	blood
28	chr3:42621800-42622800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:42621800-42622800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:42621800-42622800	Enhancers	Liver	Liver
31	chr3:42621800-42622800	Flanking Active TSS	NHEK	skin
32	chr3:42621800-42623000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:42621800-42623000	Flanking Active TSS	Dnd41	blood
34	chr3:42622000-42622800	Enhancers	Primary T cells from cord blood	blood
35	chr3:42622000-42622800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:42622000-42622800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:42622000-42622800	Flanking Active TSS	HUVEC	blood vessel
38	chr3:42622000-42624600	Active TSS	A549	lung
39	chr3:42622200-42622800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr3:42622200-42622800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:42622200-42622800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr3:42622200-42622800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr3:42622200-42622800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:42622200-42622800	Flanking Active TSS	Hela-S3	cervix
45	chr3:42622200-42622800	Flanking Active TSS	Osteobl	bone
46	chr3:42622200-42623000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr3:42622200-42623000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr3:42622200-42623000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:42622200-42623000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:42622200-42623000	Flanking Active TSS	Brain Substantia Nigra	brain

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