Variant report

Variant	rs409858
Chromosome Location	chr13:111154061-111154062
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	chr13:111152980..111156957-chr13:111159190..111161050,4	MCF-7	breast:
2	chr13:111152581..111154203-chr13:111156626..111159489,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134871	Chromatin interaction
ENSG00000232814	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13378377	1.00[MEX][hapmap]
rs383468	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs405044	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs406174	0.90[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs414604	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs439831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4771683	0.90[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs4771684	0.89[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv430604	chr13:111095999-111156999	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv901009	chr13:111134780-111176393	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
9	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111109000-111158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr13:111109600-111155800	Strong transcription	Fetal Intestine Large	intestine
3	chr13:111109600-111158800	Strong transcription	Ovary	ovary
4	chr13:111109800-111168000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr13:111119200-111159200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr13:111119600-111160400	Weak transcription	Brain Germinal Matrix	brain
7	chr13:111124400-111167400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr13:111125600-111157800	Weak transcription	Small Intestine	intestine
9	chr13:111127600-111156200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr13:111130600-111155400	Strong transcription	Left Ventricle	heart
11	chr13:111131000-111162800	Weak transcription	Fetal Brain Male	brain
12	chr13:111131400-111158000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr13:111131800-111159400	Weak transcription	Esophagus	oesophagus
14	chr13:111132200-111158400	Strong transcription	Colon Smooth Muscle	Colon
15	chr13:111132200-111158600	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:111138800-111155400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr13:111139600-111157800	Strong transcription	Placenta	Placenta
18	chr13:111139600-111166400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:111139600-111166600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr13:111139800-111155400	Strong transcription	Right Ventricle	heart
21	chr13:111139800-111155600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr13:111139800-111158000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr13:111140200-111167200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr13:111140800-111166600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:111141000-111159000	Strong transcription	NHLF	lung
26	chr13:111141600-111165600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr13:111141800-111155400	Strong transcription	Spleen	Spleen
28	chr13:111143200-111156400	Weak transcription	Stomach Mucosa	stomach
29	chr13:111143400-111166800	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr13:111143600-111159000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr13:111145200-111155800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr13:111145800-111160200	Weak transcription	Psoas Muscle	Psoas
33	chr13:111146800-111156200	Strong transcription	HSMM	muscle
34	chr13:111147000-111158800	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr13:111147000-111159400	Strong transcription	Fetal Lung	lung
36	chr13:111147200-111159000	Strong transcription	Aorta	Aorta
37	chr13:111147800-111156600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr13:111148000-111156200	Strong transcription	HSMMtube	muscle
39	chr13:111148600-111155200	Strong transcription	Fetal Kidney	kidney
40	chr13:111149600-111156000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr13:111149600-111156600	Strong transcription	Lung	lung
42	chr13:111149600-111159000	Strong transcription	Fetal Stomach	stomach
43	chr13:111149600-111161800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr13:111149800-111155600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr13:111149800-111156400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr13:111149800-111162400	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr13:111150000-111154200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr13:111150000-111159200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr13:111150000-111165000	Weak transcription	Brain Angular Gyrus	brain
50	chr13:111150600-111155600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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