Variant report

Variant	rs684119
Chromosome Location	chr6:33662667-33662668
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	chr6:33661582-33663177	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:33662575-33664313	K562	blood:	n/a	n/a
3	POLR2A	chr6:33662091-33663836	K562	blood:	n/a	n/a
4	FOS	chr6:33662474-33662752	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr6:33662045-33662757	HUVEC	blood vessel:	n/a	n/a
6	STAT3	chr6:33662433-33662759	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr6:33660657-33663799	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:33662654-33662691	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:33661956-33663057	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr6:33662026-33666005	Hela-S3	cervix:	n/a	n/a
11	FOS	chr6:33662377-33662779	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr6:33662069-33664724	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:33662113-33666054	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:33660869-33664890	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:33662582-33662717	ProgFib	skin:	n/a	n/a
16	POLR2A	chr6:33662019-33665616	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr6:33657437-33666414	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr6:33662092-33663172	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:33662395-33662868	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:33662094-33663781	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr6:33662182-33664245	K562	blood:	n/a	n/a
22	POLR2A	chr6:33661275-33663273	MCF-7	breast:	n/a	n/a
23	POLR2A	chr6:33662121-33662746	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr6:33662046-33663019	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr6:33662121-33662782	HCT-116	colon:	n/a	n/a
26	STAT3	chr6:33662401-33662744	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr6:33662424-33662680	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr6:33662027-33662734	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr6:33661893-33662686	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr6:33658911-33667009	K562	blood:	n/a	n/a
31	STAT3	chr6:33662427-33662772	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr6:33662086-33663570	PFSK-1	brain:	n/a	n/a
33	MYC	chr6:33662065-33662705	MCF10A-Er-Src	breast:	n/a	chr6:33662307-33662316 chr6:33662208-33662216 chr6:33662663-33662672
34	POLR2A	chr6:33662650-33663088	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr6:33661569-33663151	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr6:33662149-33663255	PBDE	blood:	n/a	n/a
37	POLR2A	chr6:33661859-33662875	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr6:33662639-33664943	HCT-116	colon:	n/a	n/a
39	POLR2A	chr6:33658928-33664260	K562	blood:	n/a	n/a
40	POLR2A	chr6:33662166-33662720	U87	brain:	n/a	n/a
41	FOS	chr6:33662396-33662721	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr6:33657421-33665985	SK-N-MC	brain:	n/a	n/a
43	FOS	chr6:33661923-33662764	HUVEC	blood vessel:	n/a	chr6:33662331-33662340
44	GATA2	chr6:33661899-33662894	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr6:33662160-33662726	U87	brain:	n/a	n/a
46	FOS	chr6:33662008-33662759	MCF10A-Er-Src	breast:	n/a	chr6:33662331-33662340

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
2	chr6:33377496..33379251-chr6:33661661..33664420,2	MCF-7	breast:

Variant related genes	Relation type
MIR3934	TF binding region
ENSG00000137288	Chromatin interaction
ENSG00000112511	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10947428	0.84[CEU][hapmap]
rs10947436	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1536501	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1998949	1.00[JPT][hapmap]
rs2182659	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2395401	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2395448	1.00[JPT][hapmap]
rs2967	0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4711350	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs498114	0.92[ASW][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs530614	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs549652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597386	0.92[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs597723	0.83[ASN][1000 genomes]
rs602399	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs608971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs623813	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs652049	0.89[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs654682	0.87[ASW][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs658087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680608	0.89[EUR][1000 genomes]
rs688209	0.84[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6913517	1.00[JPT][hapmap]
rs6915136	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs751727	1.00[JPT][hapmap]
rs764753	1.00[JPT][hapmap]
rs943463	1.00[JPT][hapmap]
rs943464	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs943472	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs9461905	1.00[JPT][hapmap]
rs9469542	1.00[JPT][hapmap]

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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs684119	UHRF1BP1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:33629000-33662800	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:33655000-33663600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:33655600-33664800	Weak transcription	Aorta	Aorta
13	chr6:33656400-33666000	Genic enhancers	Spleen	Spleen
14	chr6:33658000-33663400	Genic enhancers	Right Ventricle	heart
15	chr6:33658000-33667200	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr6:33658200-33666600	Genic enhancers	Fetal Muscle Leg	muscle
17	chr6:33658600-33663400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:33658600-33666400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:33659000-33666600	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr6:33659200-33665200	Genic enhancers	HMEC	breast
21	chr6:33659200-33665400	Genic enhancers	NHDF-Ad	bronchial
22	chr6:33659200-33665800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:33659200-33666600	Enhancers	Right Atrium	heart
24	chr6:33659400-33663000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:33659400-33663000	Genic enhancers	NHLF	lung
26	chr6:33659400-33663600	Enhancers	Psoas Muscle	Psoas
27	chr6:33659400-33663800	Enhancers	HSMMtube	muscle
28	chr6:33659400-33664200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:33659400-33665000	Genic enhancers	Duodenum Mucosa	Duodenum
30	chr6:33659400-33666400	Genic enhancers	Fetal Thymus	thymus
31	chr6:33659400-33668400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:33659600-33662800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:33659600-33663000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:33659600-33663600	Enhancers	NH-A	brain
35	chr6:33659600-33664600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:33659600-33665600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:33659600-33666400	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:33659600-33667000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr6:33659800-33663200	Genic enhancers	Osteobl	bone
40	chr6:33659800-33664800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:33659800-33665600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:33659800-33666000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr6:33659800-33666600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:33659800-33666600	Genic enhancers	Fetal Stomach	stomach
45	chr6:33660000-33662800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:33660000-33664600	Enhancers	Primary B cells from cord blood	blood
47	chr6:33660000-33666200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr6:33660200-33663800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:33660200-33665600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:33660200-33667200	Genic enhancers	Lung	lung

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