Variant report

Variant	rs1872165
Chromosome Location	chr3:47464757-47464758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47464416-47464778	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:47464365-47464891	K562	blood:	n/a	n/a
3	POLR2A	chr3:47460192-47464924	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47421777..47424260-chr3:47463551..47466510,3	MCF-7	breast:
2	chr3:47461509..47464905-chr3:47467197..47468812,4	K562	blood:
3	chr3:47462501..47465704-chr3:47552223..47556756,6	MCF-7	breast:
4	chr3:47457279..47459600-chr3:47464397..47467403,3	K562	blood:
5	chr3:47451174..47454005-chr3:47464334..47466551,2	K562	blood:

No data

Variant related genes	Relation type
SCAP	TF binding region
ENSG00000260236	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000163832	Chromatin interaction
ENSG00000114650	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	1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[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]
rs10865947	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1091068	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11707272	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];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[TSI][hapmap];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[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[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[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];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[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];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	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];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	0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];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[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];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[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];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[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];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[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442068	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];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	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs6778673	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];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	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];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	0.90[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs900694	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs903538	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs924009	0.89[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	chr3:47448400-47466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:47451400-47466400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:47454600-47466800	Weak transcription	Psoas Muscle	Psoas
6	chr3:47456000-47473000	Strong transcription	Thymus	Thymus
7	chr3:47459200-47465200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:47459600-47470000	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr3:47460400-47470400	Strong transcription	NHEK	skin
10	chr3:47461000-47466600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:47461200-47465400	Genic enhancers	Right Ventricle	heart
12	chr3:47461800-47467000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:47461800-47478800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:47462000-47464800	Genic enhancers	Spleen	Spleen
15	chr3:47462200-47464800	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr3:47462400-47464800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:47462400-47464800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:47462400-47465400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:47462400-47467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:47462600-47465600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:47462600-47465800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:47462600-47466800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:47462800-47465800	Genic enhancers	HepG2	liver
24	chr3:47462800-47466800	Enhancers	Stomach Mucosa	stomach
25	chr3:47463000-47469800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:47463000-47470200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:47463000-47470600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:47463200-47465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:47463200-47465200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:47463200-47465200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:47463200-47465400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:47463200-47465400	Strong transcription	Fetal Intestine Large	intestine
34	chr3:47463200-47465600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:47463200-47465800	Weak transcription	Fetal Lung	lung
36	chr3:47463200-47466000	Weak transcription	HMEC	breast
37	chr3:47463200-47466800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:47463200-47467800	Strong transcription	Aorta	Aorta
39	chr3:47463200-47468400	Weak transcription	Osteobl	bone
40	chr3:47463200-47470200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:47463200-47470400	Strong transcription	Brain Germinal Matrix	brain
42	chr3:47463200-47470600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:47463200-47472800	Weak transcription	HUVEC	blood vessel
44	chr3:47463200-47472800	Weak transcription	NHDF-Ad	bronchial
45	chr3:47463200-47473000	Weak transcription	NH-A	brain
46	chr3:47463200-47474400	Weak transcription	Fetal Kidney	kidney
47	chr3:47463400-47465200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:47463400-47465200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:47463400-47465400	Enhancers	Liver	Liver
50	chr3:47463400-47465800	Strong transcription	Fetal Intestine Small	intestine

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