Variant report

Variant	rs1017468
Chromosome Location	chr3:139145778-139145779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139140366..139142053-chr3:139144253..139146532,2	K562	blood:
2	chr3:139145144..139147566-chr3:139278645..139281496,3	MCF-7	breast:
3	chr3:139107265..139110435-chr3:139143969..139145839,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184432	Chromatin interaction
ENSG00000248932	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1080371	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13084900	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1580642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167187	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs169824	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176982	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176983	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176985	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs176987	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs184155	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs186103	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs188420	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs188421	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071388	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2083336	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2118981	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs295469	0.84[EUR][1000 genomes]
rs295470	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295471	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295473	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs295474	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs295478	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs295479	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs295481	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs295482	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs295484	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs407958	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs432387	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4607068	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683463	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683464	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57357132	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439856	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439860	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6771831	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6772199	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6784684	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6787649	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6803593	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7375091	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7624321	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7652860	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9826544	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9833307	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9859864	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2760754	chr3:139144615-139164874	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139114200-139153800	Weak transcription	Left Ventricle	heart
2	chr3:139136400-139166200	Weak transcription	Fetal Brain Female	brain
3	chr3:139137200-139149200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:139137400-139146400	Weak transcription	Primary T cells from cord blood	blood
5	chr3:139137600-139146400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:139137800-139153200	Weak transcription	Esophagus	oesophagus
7	chr3:139138200-139153600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:139138400-139146600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:139138600-139147800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:139138600-139166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:139138600-139170400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:139139600-139160000	Weak transcription	Fetal Brain Male	brain
13	chr3:139140400-139146400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:139140400-139146600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:139140400-139146600	Weak transcription	Brain Angular Gyrus	brain
16	chr3:139140600-139146600	Weak transcription	Fetal Kidney	kidney
17	chr3:139140600-139147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:139140800-139147200	Weak transcription	Brain Germinal Matrix	brain
19	chr3:139140800-139152800	Weak transcription	Placenta	Placenta
20	chr3:139140800-139153200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:139140800-139153200	Weak transcription	HSMMtube	muscle
22	chr3:139140800-139153800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:139141200-139160000	Weak transcription	Lung	lung
24	chr3:139141400-139146800	Weak transcription	Fetal Intestine Large	intestine
25	chr3:139141400-139167000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:139142000-139146600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:139142000-139146600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:139142000-139147400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:139142200-139146600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:139142200-139152800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:139142200-139172200	Weak transcription	Fetal Heart	heart
32	chr3:139142400-139154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:139142600-139149400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:139142600-139158200	Weak transcription	Gastric	stomach
35	chr3:139142800-139146400	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:139142800-139149400	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:139142800-139150400	Weak transcription	Spleen	Spleen
38	chr3:139142800-139162600	Weak transcription	Psoas Muscle	Psoas
39	chr3:139142800-139169000	Weak transcription	Aorta	Aorta
40	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
41	chr3:139143000-139146600	Weak transcription	Fetal Intestine Small	intestine
42	chr3:139143000-139153800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:139143400-139146200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:139143400-139152000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:139143600-139153800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:139144400-139147000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:139144600-139148400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:139144800-139145800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:139144800-139146600	Weak transcription	Adipose Nuclei	Adipose
50	chr3:139144800-139151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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