Variant report

Variant	rs13361218
Chromosome Location	chr5:58470077-58470078
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:58329837..58331265-chr5:58469751..58470698,8	MCF-7	breast:
2	chr5:58182290..58183191-chr5:58469771..58470690,2	MCF-7	breast:
3	chr5:58187094..58187737-chr5:58469769..58470270,2	MCF-7	breast:
4	chr5:58329956..58330645-chr5:58469795..58470725,3	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10472093	0.82[EUR][1000 genomes]
rs13176291	0.90[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs13176475	0.90[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs1559251	1.00[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1824788	0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs1971940	0.90[CEU][hapmap];0.90[MEX][hapmap]
rs28385324	0.82[CEU][hapmap];0.95[MEX][hapmap]
rs6450506	1.00[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6875867	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs716908	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7728050	0.90[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs889229	0.80[GIH][hapmap]
rs922434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292193	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv881702	chr5:58432413-58474854	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13361218	CCNO	cis	parietal	SCAN
rs13361218	LRRC70	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
2	chr5:58447600-58473200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58447600-58473400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:58447600-58479600	Weak transcription	Left Ventricle	heart
5	chr5:58449400-58473600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:58449800-58489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:58454400-58472800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:58455200-58473400	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:58455800-58473600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:58457800-58473400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:58459400-58473400	Weak transcription	Fetal Stomach	stomach
12	chr5:58460000-58472600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:58461000-58484200	Weak transcription	HUVEC	blood vessel
14	chr5:58464200-58484000	Weak transcription	Brain Anterior Caudate	brain
15	chr5:58464200-58485400	Weak transcription	Aorta	Aorta
16	chr5:58464400-58473000	Weak transcription	Right Ventricle	heart
17	chr5:58464600-58474400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:58464800-58478800	Weak transcription	Hela-S3	cervix
19	chr5:58465600-58470400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:58466000-58472800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:58466000-58473600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:58466200-58473600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:58466200-58474400	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:58466200-58479400	Weak transcription	Psoas Muscle	Psoas
25	chr5:58467200-58474800	Weak transcription	Esophagus	oesophagus
26	chr5:58469000-58483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:58469200-58484400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:58469400-58470400	Enhancers	Primary T cells from cord blood	blood
29	chr5:58469800-58470200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:58469800-58473600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:58469800-58477000	Genic enhancers	A549	lung
32	chr5:58469800-58478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:58470000-58470200	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr5:58470000-58472800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:58470000-58472800	Weak transcription	Fetal Intestine Large	intestine
36	chr5:58470000-58473800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:58470000-58483400	Weak transcription	Fetal Lung	lung

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