Variant report

Variant	rs1024036
Chromosome Location	chr3:47317665-47317666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47204839..47206673-chr3:47316671..47318992,2	K562	blood:
2	chr3:47315110..47317997-chr3:47321683..47324760,3	MCF-7	breast:
3	chr3:47308250..47310390-chr3:47316746..47318769,2	MCF-7	breast:
4	chr3:47308440..47310192-chr3:47315803..47317741,2	K562	blood:

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

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1038393	1.00[EUR][1000 genomes]
rs10865945	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865947	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs1091068	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11707272	1.00[EUR][1000 genomes]
rs11708257	1.00[EUR][1000 genomes]
rs11709693	1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	1.00[EUR][1000 genomes]
rs12330516	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12491029	0.93[YRI][hapmap]
rs12631697	1.00[EUR][1000 genomes]
rs12631730	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs13077134	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs13078181	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13084060	0.87[AMR][1000 genomes]
rs13323092	0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531874	0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs1872165	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]
rs1874264	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979736	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2350642	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28735306	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295431	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs295443	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295444	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295445	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295448	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs295450	0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.82[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs295453	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.82[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs295459	1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4018904	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]
rs448018	1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4858812	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]
rs4858823	1.00[EUR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442063	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442066	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442068	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]
rs6442069	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs648226	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772449	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]
rs6775797	1.00[EUR][1000 genomes]
rs6778673	1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778687	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[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	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs6788978	1.00[EUR][1000 genomes]
rs6789730	1.00[EUR][1000 genomes]
rs6808117	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808629	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7372780	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs73831482	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615774	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630154	0.84[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7639121	0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643150	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643181	0.87[AMR][1000 genomes]
rs7644043	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]
rs7644382	0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	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]
rs7652492	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807930	0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900688	1.00[EUR][1000 genomes]
rs900689	0.89[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	1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs900694	0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs903538	1.00[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs924009	0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819475	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823480	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9826488	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827293	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828124	1.00[EUR][1000 genomes]
rs9828289	0.82[AFR][1000 genomes]
rs9828473	1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852167	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861247	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861265	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	0.87[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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47264200-47322200	Weak transcription	Gastric	stomach
2	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
4	chr3:47300800-47322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:47301000-47322800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:47301200-47323000	Weak transcription	Psoas Muscle	Psoas
7	chr3:47302600-47322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:47302800-47323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:47305600-47323200	Weak transcription	Primary T cells from cord blood	blood
10	chr3:47308600-47322200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:47308600-47322400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:47308600-47323000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:47308600-47323200	Weak transcription	Esophagus	oesophagus
14	chr3:47308800-47318000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:47308800-47322200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:47308800-47322200	Weak transcription	Hela-S3	cervix
17	chr3:47308800-47322200	Weak transcription	HepG2	liver
18	chr3:47308800-47322200	Weak transcription	NHEK	skin
19	chr3:47308800-47322400	Weak transcription	A549	lung
20	chr3:47308800-47322600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:47308800-47322600	Weak transcription	Brain Anterior Caudate	brain
22	chr3:47308800-47322600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:47308800-47322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:47308800-47322800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:47308800-47323000	Weak transcription	Adipose Nuclei	Adipose
26	chr3:47308800-47323000	Weak transcription	Brain Substantia Nigra	brain
27	chr3:47309000-47322200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:47309000-47322200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:47309000-47322400	Weak transcription	Placenta	Placenta
30	chr3:47309000-47322600	Weak transcription	HUVEC	blood vessel
31	chr3:47309000-47322800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:47309000-47322800	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:47309000-47323000	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:47309000-47323200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:47309000-47323200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:47309200-47322200	Weak transcription	K562	blood
37	chr3:47309200-47322600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:47309200-47323200	Weak transcription	HSMMtube	muscle
39	chr3:47309800-47322200	Weak transcription	Dnd41	blood
40	chr3:47311000-47322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:47311600-47322200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:47311600-47322400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:47311600-47322400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:47312000-47322400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:47312400-47323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:47312600-47322600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr3:47312600-47322800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:47314200-47319200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:47314200-47320000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:47314400-47319200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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