Variant report

Variant	rs3805726
Chromosome Location	chr5:80725640-80725641
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	chr5:80725023..80728216-chr5:80731290..80736124,4	MCF-7	breast:
2	chr5:80721446..80723519-chr5:80723791..80726002,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145687	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10036712	1.00[CHB][hapmap]
rs10041030	0.91[CHB][hapmap]
rs10042201	0.91[CHB][hapmap]
rs10042303	1.00[CHB][hapmap]
rs10075648	0.92[CHB][hapmap]
rs10474031	0.92[CHB][hapmap]
rs10942267	0.82[CHB][hapmap]
rs10942269	0.82[CHB][hapmap]
rs11739075	0.91[CHB][hapmap]
rs11740719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11949697	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12697705	0.91[CHB][hapmap]
rs1541830	0.92[CHB][hapmap]
rs2162973	0.92[CHB][hapmap]
rs34150522	0.84[ASN][1000 genomes]
rs4274955	0.82[CHB][hapmap]
rs4392600	0.82[CHB][hapmap]
rs4426897	0.82[CHB][hapmap]
rs4513668	0.82[CHB][hapmap]
rs6452412	0.92[CHB][hapmap]
rs6452415	0.92[CHB][hapmap]
rs6452419	0.82[CHB][hapmap]
rs6868422	0.92[CHB][hapmap]
rs6868748	0.92[CHB][hapmap]
rs6871860	0.84[CHB][hapmap]
rs6872775	0.91[CHB][hapmap]
rs6874029	0.82[CHB][hapmap]
rs6877102	0.92[CHB][hapmap]
rs6880200	0.82[CHB][hapmap]
rs6883488	0.91[CHB][hapmap]
rs6887937	0.91[CHB][hapmap]
rs6897189	0.91[CHB][hapmap]
rs7711020	0.84[CHB][hapmap]
rs7717663	0.82[CHB][hapmap]
rs7719373	0.82[CHB][hapmap]
rs7725320	0.82[CHB][hapmap]
rs7733938	1.00[CHB][hapmap]
rs9596	0.92[CHB][hapmap]
rs964102	1.00[CHB][hapmap]

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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3805726	RASGRF2	cis	cerebellum	SCAN
rs3805726	CKMT2	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80697200-80739600	Weak transcription	Left Ventricle	heart
2	chr5:80702200-80733600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:80703200-80779200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:80704400-80747600	Weak transcription	Placenta	Placenta
5	chr5:80707400-80748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:80708000-80729400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:80709200-80755200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr5:80713600-80728200	Weak transcription	Lung	lung
9	chr5:80713600-80769200	Weak transcription	Esophagus	oesophagus
10	chr5:80716200-80767800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:80716400-80727400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr5:80716600-80730000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:80716800-80768400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:80717000-80743800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:80717200-80769200	Weak transcription	Right Ventricle	heart
16	chr5:80718000-80768800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr5:80718400-80730800	Weak transcription	Primary B cells from cord blood	blood
18	chr5:80718400-80752600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:80718400-80754800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:80718400-80755000	Weak transcription	GM12878-XiMat	blood
21	chr5:80718800-80727400	Weak transcription	Thymus	Thymus
22	chr5:80719000-80769200	Weak transcription	HSMMtube	muscle
23	chr5:80721600-80739800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:80722000-80754800	Weak transcription	HSMM	muscle
25	chr5:80722200-80730600	Weak transcription	Primary T cells from cord blood	blood
26	chr5:80722200-80731200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:80722400-80729600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:80722400-80730800	Weak transcription	Fetal Kidney	kidney
29	chr5:80722400-80746600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:80722400-80754800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:80722400-80755200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:80722400-80768800	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:80722400-80768800	Weak transcription	Fetal Brain Female	brain
34	chr5:80722600-80726000	Strong transcription	Fetal Thymus	thymus
35	chr5:80722600-80726600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:80722600-80732800	Weak transcription	Brain Angular Gyrus	brain
37	chr5:80722600-80736000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:80722600-80748600	Weak transcription	Ovary	ovary
39	chr5:80722600-80767600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:80722600-80768000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr5:80722600-80768200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:80722600-80769000	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:80722600-80769000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:80722600-80769000	Weak transcription	Fetal Brain Male	brain
45	chr5:80722600-80769000	Weak transcription	Psoas Muscle	Psoas
46	chr5:80722600-80769200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:80722800-80727400	Weak transcription	Fetal Stomach	stomach
48	chr5:80722800-80744200	Weak transcription	Adipose Nuclei	Adipose
49	chr5:80722800-80747800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:80722800-80748400	Weak transcription	Fetal Lung	lung

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