Variant report

Variant	rs10865947
Chromosome Location	chr3:47466161-47466162
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	FOXA1	chr3:47466131-47467016	HepG2	liver:	n/a	n/a
2	FOXA2	chr3:47465946-47466856	HepG2	liver:	n/a	n/a
3	RCOR1	chr3:47465851-47466708	HepG2	liver:	n/a	n/a
4	ARID3A	chr3:47466125-47466864	HepG2	liver:	n/a	n/a
5	TCF7L2	chr3:47466108-47466790	HepG2	liver:	n/a	chr3:47466372-47466381 chr3:47466371-47466381 chr3:47466370-47466384 chr3:47466369-47466385 chr3:47466369-47466385
6	POLR2A	chr3:47466126-47466182	HepG2	liver:	n/a	n/a
7	EP300	chr3:47466071-47466783	HepG2	liver:	n/a	chr3:47466440-47466450
8	POLR2A	chr3:47465174-47466254	Hela-S3	cervix:	n/a	n/a
9	MYBL2	chr3:47465997-47466622	HepG2	liver:	n/a	n/a
10	FOXA1	chr3:47466093-47467007	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:47466084-47467149	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:47466069-47466235	GM12878	blood:	n/a	n/a
13	TEAD4	chr3:47466150-47466958	HepG2	liver:	n/a	n/a
14	FOXA1	chr3:47466140-47466804	HepG2	liver:	n/a	n/a
15	EP300	chr3:47465977-47466883	HepG2	liver:	n/a	chr3:47466052-47466065 chr3:47466440-47466450
16	HDAC2	chr3:47466157-47466560	HepG2	liver:	n/a	chr3:47466441-47466450
17	SP1	chr3:47466112-47466686	HepG2	liver:	n/a	chr3:47466391-47466404
18	FOXA2	chr3:47466102-47466931	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47421777..47424260-chr3:47463551..47466510,3	MCF-7	breast:
2	chr3:47465309..47466816-chr3:47468735..47471629,2	K562	blood:
3	chr3:47457279..47459600-chr3:47464397..47467403,3	K562	blood:
4	chr3:47465805..47469012-chr3:47553458..47556919,3	K562	blood:
5	chr3:47451174..47454005-chr3:47464334..47466551,2	K562	blood:
6	chr3:47465811..47468194-chr3:47471734..47473557,2	K562	blood:
7	chr3:47462068..47464765-chr3:47465209..47466944,2	MCF-7	breast:

Variant related genes	Relation type
SCAP	TF binding region
ENSG00000260236	Chromatin interaction
ENSG00000114650	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1024036	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs1038393	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs1091068	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11707272	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12491029	1.00[YRI][hapmap]
rs12631697	1.00[EUR][1000 genomes]
rs13077134	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs1531874	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2170814	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs295431	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448018	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858812	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858855	1.00[AMR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442066	1.00[EUR][1000 genomes]
rs6442068	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648226	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs6778673	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6778687	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs6788978	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789730	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs7372780	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7612191	0.87[AMR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621853	0.87[AMR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7639121	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900688	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900689	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900690	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900693	0.88[YRI][hapmap]
rs900694	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs903538	1.00[YRI][hapmap]
rs924009	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9828124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:47451400-47466400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:47454600-47466800	Weak transcription	Psoas Muscle	Psoas
5	chr3:47456000-47473000	Strong transcription	Thymus	Thymus
6	chr3:47459600-47470000	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr3:47460400-47470400	Strong transcription	NHEK	skin
8	chr3:47461000-47466600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:47461800-47467000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:47461800-47478800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:47462400-47467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:47462600-47466800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:47462800-47466800	Enhancers	Stomach Mucosa	stomach
14	chr3:47463000-47469800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:47463000-47470200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:47463000-47470600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:47463200-47466800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:47463200-47467800	Strong transcription	Aorta	Aorta
20	chr3:47463200-47468400	Weak transcription	Osteobl	bone
21	chr3:47463200-47470200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:47463200-47470400	Strong transcription	Brain Germinal Matrix	brain
23	chr3:47463200-47470600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:47463200-47472800	Weak transcription	HUVEC	blood vessel
25	chr3:47463200-47472800	Weak transcription	NHDF-Ad	bronchial
26	chr3:47463200-47473000	Weak transcription	NH-A	brain
27	chr3:47463200-47474400	Weak transcription	Fetal Kidney	kidney
28	chr3:47463400-47470200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:47463400-47470200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:47463400-47470400	Strong transcription	Placenta	Placenta
31	chr3:47463400-47470600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:47463400-47471200	Weak transcription	Fetal Brain Male	brain
33	chr3:47463400-47475400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:47463400-47477600	Strong transcription	Fetal Thymus	thymus
35	chr3:47463400-47484600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:47463600-47468800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:47463600-47470200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:47463600-47470400	Strong transcription	Brain Anterior Caudate	brain
39	chr3:47463600-47471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:47463600-47472400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:47463600-47476800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:47463600-47476800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:47463600-47484800	Strong transcription	Primary T cells from cord blood	blood
44	chr3:47463800-47470000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:47463800-47470400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:47463800-47471400	Strong transcription	Fetal Brain Female	brain
47	chr3:47463800-47472800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:47463800-47473000	Strong transcription	Fetal Stomach	stomach
49	chr3:47463800-47476800	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:47463800-47479400	Weak transcription	A549	lung

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