Variant report

Variant	rs6778687
Chromosome Location	chr3:47300708-47300709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47299223..47301874-chr3:47323863..47326693,2	K562	blood:
2	chr3:47299450..47301469-chr3:47310595..47313090,2	K562	blood:

Variant related genes	Relation type
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1024036	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1038393	1.00[EUR][1000 genomes]
rs10865945	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865947	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs1091068	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11130122	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11706212	1.00[EUR][1000 genomes]
rs11707272	1.00[EUR][1000 genomes]
rs11708257	1.00[EUR][1000 genomes]
rs11709693	1.00[EUR][1000 genomes]
rs11719129	0.83[AFR][1000 genomes]
rs11922925	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11928558	1.00[EUR][1000 genomes]
rs12330516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12491254	0.81[AFR][1000 genomes]
rs12631697	1.00[EUR][1000 genomes]
rs12631730	0.95[YRI][hapmap]
rs13062185	1.00[EUR][1000 genomes]
rs13077134	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs13078181	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13079174	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13079416	1.00[EUR][1000 genomes]
rs13082531	1.00[EUR][1000 genomes]
rs13084060	1.00[AMR][1000 genomes]
rs13323092	0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473382	1.00[EUR][1000 genomes]
rs1531874	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs1814564	1.00[EUR][1000 genomes]
rs1869870	1.00[EUR][1000 genomes]
rs1872165	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs1874264	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979736	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2350642	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28735306	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295431	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295444	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295448	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4018904	0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4282092	1.00[EUR][1000 genomes]
rs4478107	1.00[EUR][1000 genomes]
rs448018	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	1.00[EUR][1000 genomes]
rs4682833	1.00[EUR][1000 genomes]
rs4683277	1.00[EUR][1000 genomes]
rs4683279	1.00[EUR][1000 genomes]
rs4858812	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs4858823	1.00[EUR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442063	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442066	1.00[EUR][1000 genomes]
rs6442068	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs6442069	1.00[EUR][1000 genomes]
rs648226	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772449	0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6778673	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6780994	1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	1.00[EUR][1000 genomes]
rs6787210	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6788978	1.00[EUR][1000 genomes]
rs6789730	1.00[EUR][1000 genomes]
rs6808117	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7372780	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs73831482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615774	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630154	0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7639121	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643150	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643181	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7643868	1.00[EUR][1000 genomes]
rs7644043	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs7644382	0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807930	0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900688	1.00[EUR][1000 genomes]
rs900689	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs900690	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	1.00[EUR][1000 genomes]
rs900693	0.85[YRI][hapmap]
rs900694	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs903538	0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs924009	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	1.00[EUR][1000 genomes]
rs936179	1.00[EUR][1000 genomes]
rs936180	1.00[EUR][1000 genomes]
rs936181	1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9826488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828124	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9828289	0.80[AFR][1000 genomes]
rs9828473	0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861247	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9990284	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	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47264200-47322200	Weak transcription	Gastric	stomach
2	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:47276400-47305200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:47285400-47315800	Weak transcription	Pancreas	Pancrea
8	chr3:47285600-47312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:47293600-47302800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
11	chr3:47298000-47302000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:47299400-47308200	Weak transcription	Right Atrium	heart
13	chr3:47299600-47301800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:47299600-47307800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:47299800-47301000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:47300200-47301200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:47300400-47301000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr3:47300400-47301000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:47300400-47301000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:47300400-47301000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:47300400-47301000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:47300400-47301000	Enhancers	Fetal Intestine Small	intestine
23	chr3:47300400-47301400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:47300600-47300800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:47300600-47300800	Enhancers	HSMMtube	muscle
26	chr3:47300600-47301000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:47300600-47301000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:47300600-47301000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr3:47300600-47301000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:47300600-47301000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:47300600-47301000	Enhancers	Fetal Intestine Large	intestine
32	chr3:47300600-47301000	Enhancers	Placenta	Placenta
33	chr3:47300600-47301000	Enhancers	Lung	lung
34	chr3:47300600-47301000	Flanking Active TSS	HepG2	liver
35	chr3:47300600-47301200	Enhancers	HUES48 Cell Line	embryonic stem cell

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