Variant report

Variant	rs7728050
Chromosome Location	chr5:58465400-58465401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1105577	0.83[CHB][hapmap]
rs12658004	0.84[ASN][1000 genomes]
rs13176291	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs13176475	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs13361218	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]
rs1559251	0.90[CEU][hapmap];0.91[MEX][hapmap]
rs16889280	0.83[CHB][hapmap]
rs1824788	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1862563	0.82[CHB][hapmap]
rs1971940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28385324	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4700322	0.80[EUR][1000 genomes]
rs55730818	0.81[ASN][1000 genomes]
rs55998224	0.81[ASN][1000 genomes]
rs6450506	0.90[CEU][hapmap];0.91[MEX][hapmap]
rs6877743	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs716908	0.90[CEU][hapmap]
rs7707065	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7730750	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs922434	0.90[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7728050	LRRC70	cis	cerebellum	SCAN
rs7728050	IPO11	cis	cerebellum	SCAN
rs7728050	CCNO	cis	parietal	SCAN

Chromatin state (count:34 , 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	chr5:58460800-58469400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:58461000-58484200	Weak transcription	HUVEC	blood vessel
15	chr5:58461600-58467000	Genic enhancers	A549	lung
16	chr5:58463800-58466200	Enhancers	Colon Smooth Muscle	Colon
17	chr5:58464000-58465600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:58464200-58465400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:58464200-58484000	Weak transcription	Brain Anterior Caudate	brain
20	chr5:58464200-58485400	Weak transcription	Aorta	Aorta
21	chr5:58464400-58465400	Weak transcription	Psoas Muscle	Psoas
22	chr5:58464400-58465600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:58464400-58465800	Enhancers	HSMM	muscle
24	chr5:58464400-58465800	Enhancers	HSMMtube	muscle
25	chr5:58464400-58473000	Weak transcription	Right Ventricle	heart
26	chr5:58464600-58474400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:58464800-58478800	Weak transcription	Hela-S3	cervix
28	chr5:58465000-58466000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr5:58465200-58465600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr5:58465400-58465600	Enhancers	Rectal Smooth Muscle	rectum
31	chr5:58465400-58465600	Enhancers	Right Atrium	heart
32	chr5:58465400-58465800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr5:58465400-58466000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr5:58465400-58466200	Enhancers	Psoas Muscle	Psoas

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