Variant report

Variant	rs559847
Chromosome Location	chr13:96705160-96705161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:16970980..16971545-chr13:96704941..96705920,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000215908	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1093275	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1707244	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2389568	0.85[AFR][1000 genomes]
rs3101572	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3125432	1.00[EUR][1000 genomes]
rs3125437	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs478025	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs481049	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs481124	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs509323	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs519826	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs524961	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs530195	1.00[EUR][1000 genomes]
rs534493	1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs545894	0.85[AFR][1000 genomes]
rs548964	1.00[EUR][1000 genomes]
rs555120	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs562356	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs574109	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs592640	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs687921	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7982873	0.85[AFR][1000 genomes]
rs816137	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs816138	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs816141	1.00[ASW][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9525075	1.00[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9525076	0.94[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9584345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv900936	chr13:96697209-97032483	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96703800-96706200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:96704000-96706400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr13:96704200-96705200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr13:96704200-96706200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:96704200-96706200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr13:96704200-96707000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr13:96704400-96705200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:96704400-96706200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr13:96704400-96706200	Active TSS	Fetal Kidney	kidney
10	chr13:96704400-96706200	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr13:96704400-96707200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr13:96704600-96705200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:96704600-96705200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr13:96704600-96705200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr13:96704600-96705200	Flanking Active TSS	HUVEC	blood vessel
16	chr13:96704600-96705400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr13:96704600-96706000	Active TSS	HepG2	liver
18	chr13:96704600-96706200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr13:96704600-96706200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:96704600-96706200	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr13:96704600-96706200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:96704600-96706200	Active TSS	Brain Hippocampus Middle	brain
23	chr13:96704600-96706200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:96704600-96706200	Active TSS	Psoas Muscle	Psoas
25	chr13:96704600-96706200	Active TSS	Rectal Smooth Muscle	rectum
26	chr13:96704600-96706200	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr13:96704600-96706200	Active TSS	A549	lung
28	chr13:96704600-96706200	Active TSS	K562	blood
29	chr13:96704600-96706200	Active TSS	NHDF-Ad	bronchial
30	chr13:96704600-96706400	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr13:96704600-96706400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr13:96704600-96706400	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr13:96704600-96706600	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr13:96704600-96706600	Active TSS	HMEC	breast
35	chr13:96704600-96706600	Active TSS	NHEK	skin
36	chr13:96704600-96706800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr13:96704800-96705200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:96704800-96705200	Flanking Active TSS	Liver	Liver
39	chr13:96704800-96705200	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr13:96704800-96705200	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr13:96704800-96705200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr13:96704800-96705200	Active TSS	Fetal Brain Female	brain
43	chr13:96704800-96705200	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr13:96704800-96705200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr13:96704800-96705200	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr13:96704800-96705200	Flanking Active TSS	HSMMtube	muscle
47	chr13:96704800-96705200	Flanking Active TSS	NH-A	brain
48	chr13:96704800-96705400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr13:96704800-96706000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr13:96704800-96706000	Active TSS	Fetal Heart	heart

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