Variant report

Variant	rs2059209
Chromosome Location	chr5:95197615-95197616
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	chr1:154975787..154976600-chr5:95197599..95198316,2	Hela-S3	cervix:
2	chr5:95195786..95198605-chr5:95296132..95297926,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf27-2	chr5:95197490-95197781	ENSG00000250362.1
2	lnc-C5orf27-2	chr5:95197510-95197781	ENSG00000250362.1
3	lnc-C5orf27-2	chr5:95197487-95197781	NONHSAT102871

Variant related genes	Relation type
ENSG00000118985	Chromatin interaction
ENSG00000251314	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10476660	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs12659828	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs17085209	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2059210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248340	0.83[CHB][hapmap]
rs248341	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs6888848	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
2	chr5:95192000-95201400	Enhancers	Placenta	Placenta
3	chr5:95192200-95199400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:95192400-95199200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:95194000-95200800	Weak transcription	Gastric	stomach
6	chr5:95194200-95199000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:95194200-95203000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr5:95194800-95199400	Enhancers	Liver	Liver
9	chr5:95195000-95198400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:95195000-95198400	Weak transcription	Colonic Mucosa	Colon
11	chr5:95195000-95199000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:95195000-95200200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:95195000-95200600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:95195000-95206400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:95195000-95208400	Weak transcription	Ovary	ovary
16	chr5:95195200-95198800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:95195200-95199000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:95195200-95200600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:95195200-95217400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:95195400-95199200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr5:95195400-95199200	Enhancers	NHEK	skin
22	chr5:95195400-95201600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:95195600-95198800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:95195600-95198800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:95195600-95199000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:95195600-95199000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:95195600-95206200	Weak transcription	Brain Anterior Caudate	brain
28	chr5:95195800-95197800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:95195800-95198000	Weak transcription	Aorta	Aorta
30	chr5:95195800-95198400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:95195800-95199000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:95195800-95199000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:95195800-95199600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:95195800-95201000	Weak transcription	Brain Substantia Nigra	brain
35	chr5:95195800-95201200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr5:95195800-95201200	Enhancers	NHLF	lung
37	chr5:95196000-95198800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:95196000-95198800	Weak transcription	Esophagus	oesophagus
39	chr5:95196000-95199000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:95196200-95198600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:95196600-95197800	Enhancers	Primary hematopoietic stem cells	blood
42	chr5:95196600-95197800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr5:95196600-95199200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:95196600-95199600	Enhancers	Primary B cells from cord blood	blood
45	chr5:95196800-95197800	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr5:95196800-95197800	Enhancers	Fetal Kidney	kidney
47	chr5:95196800-95197800	Flanking Active TSS	HSMMtube	muscle
48	chr5:95196800-95197800	Flanking Active TSS	Osteobl	bone
49	chr5:95196800-95198000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr5:95196800-95198200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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