Variant report

Variant	rs900689
Chromosome Location	chr3:47452087-47452088
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47450663..47453382-chr3:47461645..47463185,2	MCF-7	breast:
2	chr3:47451733..47454199-chr3:47553714..47555598,2	K562	blood:
3	chr3:47451174..47454005-chr3:47464334..47466551,2	K562	blood:
4	chr3:47434120..47436973-chr3:47451029..47453038,2	K562	blood:
5	chr3:47451769..47453360-chr3:47455312..47457238,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163832	Chromatin interaction
ENSG00000114650	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1024036	0.89[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	0.94[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	0.94[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	0.93[YRI][hapmap]
rs12631697	1.00[EUR][1000 genomes]
rs13077134	0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1531874	0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	0.94[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	0.94[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	0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	0.94[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	0.94[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.94[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	0.94[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	0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.94[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	0.94[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	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	0.93[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	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	0.91[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	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs6778687	0.94[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	0.94[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	0.94[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	0.94[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	0.94[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]
rs900690	0.94[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	0.83[YRI][hapmap]
rs900694	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs903538	0.94[YRI][hapmap]
rs924009	0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9828124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv3425748	chr3:47451198-47453496	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3340758	chr3:47451598-47453046	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47436000-47454600	Weak transcription	Hela-S3	cervix
3	chr3:47436200-47462000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:47436600-47454800	Weak transcription	Fetal Kidney	kidney
5	chr3:47437600-47453400	Weak transcription	Psoas Muscle	Psoas
6	chr3:47437800-47462800	Weak transcription	Fetal Brain Male	brain
7	chr3:47439200-47455000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:47441400-47462400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:47442000-47452800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:47444800-47459400	Strong transcription	Liver	Liver
12	chr3:47445000-47462000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:47445000-47462400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:47445000-47462800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:47445600-47462800	Strong transcription	Fetal Brain Female	brain
16	chr3:47445800-47455600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:47446000-47458400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:47446000-47462200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:47446000-47462800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:47446200-47462000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:47446200-47462800	Strong transcription	Dnd41	blood
22	chr3:47446400-47462800	Strong transcription	Colonic Mucosa	Colon
23	chr3:47446600-47456200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:47446600-47457400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:47446600-47462800	Strong transcription	Brain Germinal Matrix	brain
26	chr3:47446800-47459400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:47446800-47462000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:47446800-47462200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr3:47447000-47452600	Weak transcription	NHDF-Ad	bronchial
30	chr3:47447000-47453200	Weak transcription	NH-A	brain
31	chr3:47447000-47454400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:47447000-47462400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:47447000-47462400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:47447000-47462400	Weak transcription	Fetal Heart	heart
35	chr3:47447000-47462400	Strong transcription	NHLF	lung
36	chr3:47447000-47462600	Strong transcription	Fetal Stomach	stomach
37	chr3:47447200-47457400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr3:47447200-47462200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:47447200-47462400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:47447400-47457400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:47447400-47462200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:47447400-47462400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr3:47447400-47462600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:47447600-47454600	Strong transcription	Brain Cingulate Gyrus	brain
45	chr3:47447600-47454800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:47447600-47458800	Strong transcription	Rectal Smooth Muscle	rectum
47	chr3:47447600-47459000	Strong transcription	Colon Smooth Muscle	Colon
48	chr3:47447600-47459200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:47447800-47453600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr3:47447800-47453800	Strong transcription	Brain Hippocampus Middle	brain

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