Variant report

Variant	rs509323
Chromosome Location	chr13:96692938-96692939
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	chr13:96691444..96693305-chr13:96704321..96706823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102595	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1093275	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1707244	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2389568	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3101572	1.00[EUR][1000 genomes]
rs3125432	1.00[EUR][1000 genomes]
rs3125437	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs478025	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs481049	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs481124	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs519826	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs524961	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs530195	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs534493	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs545894	0.88[AFR][1000 genomes]
rs548964	1.00[EUR][1000 genomes]
rs555120	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs559847	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs562356	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs574109	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs592640	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs687921	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7982873	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs816137	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs816138	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs816141	0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9525075	0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9525076	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9584345	1.00[EUR][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	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96613200-96694200	Weak transcription	A549	lung
2	chr13:96668600-96704400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr13:96669200-96694000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:96669400-96694000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:96669400-96704600	Weak transcription	Brain Anterior Caudate	brain
6	chr13:96673000-96698400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:96673200-96693400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr13:96673400-96693000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr13:96677400-96693800	Weak transcription	Aorta	Aorta
10	chr13:96677600-96704200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr13:96677800-96693000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr13:96678400-96704400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:96678600-96698800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr13:96682800-96693000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr13:96682800-96693800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:96683400-96693400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:96683400-96704200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:96686800-96698400	Weak transcription	Fetal Lung	lung
19	chr13:96687000-96694200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr13:96687000-96698800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:96687200-96693600	Weak transcription	Fetal Intestine Small	intestine
22	chr13:96687200-96693800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr13:96687200-96693800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:96687200-96694000	Weak transcription	Gastric	stomach
25	chr13:96687200-96698800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:96687200-96698800	Weak transcription	Ovary	ovary
27	chr13:96687200-96699000	Weak transcription	Left Ventricle	heart
28	chr13:96687200-96704600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr13:96687200-96705000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:96687400-96693600	Weak transcription	Fetal Stomach	stomach
31	chr13:96687400-96693800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr13:96687400-96694200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr13:96687400-96694400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr13:96687400-96698800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr13:96687400-96699200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:96688800-96694000	Weak transcription	Fetal Muscle Leg	muscle
37	chr13:96688800-96694800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:96689200-96694000	Weak transcription	Pancreas	Pancrea
39	chr13:96689400-96693400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr13:96689400-96693400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr13:96691600-96699000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr13:96692800-96694600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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