Variant report

Variant	rs11744119
Chromosome Location	chr5:40904992-40904993
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	SMC3	chr5:40904246-40905251	HepG2	liver:	n/a	chr5:40904996-40905010
2	CTCF	chr5:40904843-40905077	SK-N-SH_RA	brain:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
3	CTCF	chr5:40904873-40905128	Lung_OC	lung:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
4	CTCF	chr5:40904920-40905070	HFF	foreskin:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
5	RAD21	chr5:40903886-40906018	SK-N-SH	brain:	n/a	chr5:40904995-40905014 chr5:40904652-40904659
6	RAD21	chr5:40904651-40905293	H1-hESC	embryonic stem cell:	n/a	chr5:40904995-40905014 chr5:40904652-40904659
7	GATA3	chr5:40904779-40905221	T-47D	breast:	n/a	chr5:40905052-40905061 chr5:40905134-40905141
8	SMC3	chr5:40904809-40905268	Hela-S3	cervix:	n/a	chr5:40904996-40905010
9	CTCF	chr5:40904856-40905143	A549	lung:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
10	CTCF	chr5:40904847-40905156	GM12878	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
11	CTCF	chr5:40904861-40905145	LNCaP	prostate:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
12	RAD21	chr5:40904834-40905215	HepG2	liver:	n/a	chr5:40904995-40905014
13	CTCF	chr5:40904900-40905050	NB4	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
14	CTCF	chr5:40904940-40905090	GM12873	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
15	CTCF	chr5:40904903-40905099	GM12891	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
16	CTCF	chr5:40904960-40905110	GM12868	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
17	RAD21	chr5:40904696-40905321	HCT-116	colon:	n/a	chr5:40904995-40905014
18	CTCF	chr5:40904910-40905107	A549	lung:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
19	CTCF	chr5:40904880-40905135	GM20000	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
20	CTCF	chr5:40904940-40905090	HPAF	blood vessel:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
21	CTCF	chr5:40904893-40905119	MCF-7	breast:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
22	CTCF	chr5:40904960-40905110	BE2_C	brain:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
23	SMC3	chr5:40904163-40905520	SK-N-SH	brain:	n/a	chr5:40904996-40905010
24	CTCF	chr5:40904866-40905129	HepG2	liver:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
25	RAD21	chr5:40904760-40905317	H1-hESC	embryonic stem cell:	n/a	chr5:40904995-40905014
26	CTCF	chr5:40904920-40905070	GM12870	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
27	CTCF	chr5:40904733-40905179	K562	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
28	RAD21	chr5:40904809-40905200	GM12878	blood:	n/a	chr5:40904995-40905014
29	CTCF	chr5:40904920-40905070	GM12873	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
30	CTCF	chr5:40904920-40905070	GM12865	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
31	RAD21	chr5:40904792-40905206	A549	lung:	n/a	chr5:40904995-40905014
32	CTCF	chr5:40904940-40905090	GM12878	blood:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
33	CTCF	chr5:40904920-40905070	Hela-S3	cervix:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
34	CTCF	chr5:40904920-40905070	HRE	kidney:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
35	GATA3	chr5:40904771-40905231	T-47D	breast:	n/a	chr5:40905052-40905061 chr5:40905134-40905141
36	CUX1	chr5:40904798-40905175	K562	blood:	n/a	n/a
37	CTCF	chr5:40904880-40905030	HCM	heart:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
38	MAFK	chr5:40904722-40905213	K562	blood:	n/a	chr5:40904756-40904770 chr5:40904757-40904768 chr5:40905130-40905145
39	CTCF	chr5:40904940-40905090	SK-N-SH_RA	brain:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
40	RAD21	chr5:40904788-40905281	SK-N-SH_RA	brain:	n/a	chr5:40904995-40905014
41	YY1	chr5:40904885-40905149	HCT-116	colon:	n/a	n/a
42	CTCF	chr5:40904910-40905105	H1-hESC	embryonic stem cell:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
43	CTCF	chr5:40904920-40905070	WERI-Rb-1	eye:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
44	CTCF	chr5:40904812-40905269	MCF-7	breast:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
45	CTCF	chr5:40904920-40905070	HEK293	kidney:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
46	CTCF	chr5:40904900-40905050	NHDF-neo	bronchial:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
47	CTCF	chr5:40904940-40905090	HCT-116	colon:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
48	CTCF	chr5:40904845-40905159	Medullo	brain:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
49	CTCF	chr5:40904940-40905090	NHEK	skin:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006
50	CTCF	chr5:40904940-40905090	HMF	breast:	n/a	chr5:40904995-40905011 chr5:40904994-40905012 chr5:40904996-40905017 chr5:40904997-40905006

No.	Distal block	Cell Line	Cell type
1	chr5:40904833..40905459-chr5:41270472..41271168,3	MCF-7	breast:
2	chr5:40904937..40905544-chr5:41641443..41642188,2	K562	blood:
3	chr5:40904256..40905017-chr5:41641481..41642261,2	MCF-7	breast:
4	chr5:40755051..40755677-chr5:40904503..40905135,2	MCF-7	breast:
5	chr5:40904832..40905544-chr5:41118009..41119184,4	MCF-7	breast:
6	chr5:40904574..40905604-chr5:41346513..41347365,3	MCF-7	breast:
7	chr5:40904836..40905424-chr5:41118089..41118768,2	MCF-7	breast:
8	chr5:40904493..40905461-chr5:40962028..40963060,5	MCF-7	breast:

Variant related genes	Relation type
C7	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10512751	0.93[CEU][hapmap];0.85[CHD][hapmap]
rs16870378	0.85[CEU][hapmap]
rs178929	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1812960	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1827364	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1910015	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122570	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271709	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2455305	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2675979	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2675981	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324056	1.00[CEU][hapmap]
rs324062	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs324064	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324070	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs324071	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324073	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3792637	1.00[CEU][hapmap];0.85[CHD][hapmap]
rs4360083	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4957358	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs59027389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60480205	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6888489	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6890698	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895317	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73088503	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73088510	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7702096	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7715597	0.94[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7725655	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881467	chr5:40869802-41008650	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2757114	chr5:40874078-41009282	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759341	chr5:40874078-41009282	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv823055	chr5:40875708-41004839	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv35077	chr5:40875843-41000671	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv830268	chr5:40897361-41138366	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40897000-40906200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:40903200-40906200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:40903600-40905600	Enhancers	Liver	Liver
4	chr5:40903600-40906600	Enhancers	Ovary	ovary
5	chr5:40903800-40905600	Enhancers	Adipose Nuclei	Adipose
6	chr5:40903800-40906000	Enhancers	Fetal Heart	heart
7	chr5:40904200-40905200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:40904200-40905400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:40904200-40905600	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr5:40904200-40905600	Enhancers	Fetal Lung	lung
11	chr5:40904400-40905400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:40904400-40905400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr5:40904400-40905400	Enhancers	Psoas Muscle	Psoas
14	chr5:40904400-40905400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr5:40904400-40905400	Enhancers	Stomach Mucosa	stomach
16	chr5:40904400-40907000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:40904600-40905000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr5:40904600-40905200	Enhancers	Fetal Kidney	kidney
19	chr5:40904600-40905400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:40904600-40909600	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:40904800-40905000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:40904800-40905200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:40904800-40905800	Enhancers	HepG2	liver

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