Variant report

Variant	rs6772449
Chromosome Location	chr3:47286227-47286228
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:47276538..47278116-chr3:47285524..47288270,2	K562	blood:
2	chr3:47285945..47288434-chr3:47322946..47325919,2	MCF-7	breast:
3	chr3:47205067..47206688-chr3:47285011..47286897,2	K562	blood:
4	chr3:47279696..47282501-chr3:47283361..47286390,3	K562	blood:
5	chr3:47285472..47289397-chr3:47290230..47292753,5	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-1	chr3:47284469-47287987	NONHSAT089488
2	lnc-KLHL18-1	chr3:47284469-47288091	ENSG00000227398.3

No data

Variant related genes	Relation type
ENSG00000227398	Chromatin interaction
ENSG00000181555	Chromatin interaction
ENSG00000239128	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1024036	0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1038393	1.00[EUR][1000 genomes]
rs10865945	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865947	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs1091068	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11130122	0.90[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	0.81[AFR][1000 genomes]
rs11922925	0.96[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	0.85[AFR][1000 genomes]
rs12631697	1.00[EUR][1000 genomes]
rs12631730	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs13062185	1.00[EUR][1000 genomes]
rs13077134	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs13078181	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13079174	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13079416	1.00[EUR][1000 genomes]
rs13082531	1.00[EUR][1000 genomes]
rs13084060	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13323092	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473382	1.00[EUR][1000 genomes]
rs1531874	0.90[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs1814564	1.00[EUR][1000 genomes]
rs1869870	1.00[EUR][1000 genomes]
rs1872165	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]
rs1874264	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979736	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2350642	0.86[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	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	0.90[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs295443	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295444	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295445	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295448	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs295450	0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.88[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs295453	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	0.90[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.88[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs295459	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4018904	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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4282092	1.00[EUR][1000 genomes]
rs4389512	1.00[EUR][1000 genomes]
rs4450857	1.00[EUR][1000 genomes]
rs4478107	1.00[EUR][1000 genomes]
rs448018	1.00[EUR][1000 genomes]
rs4522803	1.00[EUR][1000 genomes]
rs4543047	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	0.90[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]
rs4858823	1.00[EUR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442047	1.00[EUR][1000 genomes]
rs6442048	1.00[EUR][1000 genomes]
rs6442062	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442063	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442066	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442068	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]
rs6442069	1.00[EUR][1000 genomes]
rs648226	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6778673	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778687	0.95[YRI][hapmap];0.93[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	0.95[YRI][hapmap];0.90[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]
rs6806521	1.00[EUR][1000 genomes]
rs6808117	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809904	1.00[EUR][1000 genomes]
rs7372780	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs73831482	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615774	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630154	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7639121	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643150	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643181	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7643868	1.00[EUR][1000 genomes]
rs7644043	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]
rs7644382	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	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[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	0.90[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900688	1.00[EUR][1000 genomes]
rs900689	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs900690	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	1.00[EUR][1000 genomes]
rs900693	1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs900694	0.90[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs903538	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs924009	0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936177	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	1.00[EUR][1000 genomes]
rs9828473	0.89[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[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:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47262800-47287400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:47264200-47322200	Weak transcription	Gastric	stomach
3	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:47267400-47287200	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:47269800-47288400	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:47270200-47288600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:47270600-47286800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:47272600-47288200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:47276400-47305200	Weak transcription	Brain Anterior Caudate	brain
12	chr3:47277000-47288200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:47277000-47292000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:47277600-47300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:47279800-47288800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:47282200-47287000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:47282200-47291800	Weak transcription	HepG2	liver
18	chr3:47282200-47300400	Weak transcription	Fetal Intestine Small	intestine
19	chr3:47282200-47300600	Weak transcription	Lung	lung
20	chr3:47282600-47292400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:47283400-47293200	Weak transcription	Psoas Muscle	Psoas
23	chr3:47284600-47287400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:47284800-47286600	Strong transcription	Fetal Stomach	stomach
25	chr3:47284800-47300400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:47285400-47315800	Weak transcription	Pancreas	Pancrea
27	chr3:47285600-47312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:47285800-47286400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:47285800-47289800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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