Variant report

Variant	rs13320571
Chromosome Location	chr3:43334020-43334021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43326351..43330245-chr3:43331873..43336524,8	MCF-7	breast:
2	chr3:43332997..43335477-chr3:43335619..43338331,2	K562	blood:
3	chr3:43327270..43330892-chr3:43331691..43335794,4	K562	blood:

Variant related genes	Relation type
ENSG00000163788	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10865932	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634274	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap]
rs13065491	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384433	1.00[CHB][hapmap]
rs1395372	1.00[CHB][hapmap]
rs1588027	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs17075317	0.82[JPT][hapmap]
rs17075535	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075558	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075596	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17075597	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17075600	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17075630	0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap]
rs17075705	1.00[CHB][hapmap]
rs2372372	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372437	1.00[CHB][hapmap]
rs2888298	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128529	1.00[CHB][hapmap]
rs4510359	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs4682678	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682679	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682682	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682685	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs4682882	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683366	1.00[JPT][hapmap]
rs6441772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6441777	1.00[CHB][hapmap]
rs6770540	1.00[CHB][hapmap]
rs6783741	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs6791641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6800983	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs6803929	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621298	0.82[JPT][hapmap]
rs7628317	1.00[CHB][hapmap]
rs7649401	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311339	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs9681394	0.93[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs977911	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs9834842	1.00[CEU][hapmap]
rs9836386	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9857781	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv876732	chr3:43326887-43360879	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv590154	chr3:43327873-43334020	Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv590155	chr3:43327873-43334878	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv590158	chr3:43327924-43334878	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv590160	chr3:43328076-43334878	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43329200-43344800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:43329200-43346800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:43329400-43346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:43329600-43345000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:43329800-43335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:43330400-43344800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:43330600-43334800	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr3:43330800-43336400	Weak transcription	HSMMtube	muscle
9	chr3:43330800-43344600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:43330800-43359000	Weak transcription	Fetal Brain Male	brain
11	chr3:43331000-43334200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:43331000-43335400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:43331000-43340600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:43331000-43344600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:43331200-43334800	Genic enhancers	Dnd41	blood
16	chr3:43331200-43338200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:43331200-43344600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:43331400-43334600	Weak transcription	Esophagus	oesophagus
19	chr3:43331400-43338000	Weak transcription	HSMM	muscle
20	chr3:43331400-43338000	Weak transcription	K562	blood
21	chr3:43331400-43344600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:43331400-43344600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:43331400-43358200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:43331600-43335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:43331600-43338200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:43331600-43338200	Weak transcription	Brain Angular Gyrus	brain
27	chr3:43331600-43344600	Weak transcription	Placenta	Placenta
28	chr3:43331600-43344600	Weak transcription	Hela-S3	cervix
29	chr3:43331600-43344800	Weak transcription	Brain Germinal Matrix	brain
30	chr3:43331800-43339600	Enhancers	Liver	Liver
31	chr3:43332000-43334800	Enhancers	Right Ventricle	heart
32	chr3:43332000-43336000	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr3:43332200-43335000	Enhancers	Fetal Heart	heart
34	chr3:43332400-43361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:43332600-43334400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr3:43332600-43334600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr3:43332600-43335400	Enhancers	Colon Smooth Muscle	Colon
38	chr3:43332600-43336200	Weak transcription	A549	lung
39	chr3:43332600-43336600	Enhancers	Primary B cells from cord blood	blood
40	chr3:43332800-43334200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:43332800-43334200	Weak transcription	Left Ventricle	heart
42	chr3:43332800-43334600	Weak transcription	Ovary	ovary
43	chr3:43332800-43334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:43332800-43334800	Enhancers	Duodenum Mucosa	Duodenum
45	chr3:43332800-43335000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:43332800-43335000	Enhancers	HepG2	liver
47	chr3:43332800-43336000	Weak transcription	Fetal Kidney	kidney
48	chr3:43332800-43336800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:43332800-43338000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:43332800-43338000	Weak transcription	Fetal Muscle Leg	muscle

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