Variant report

Variant	rs889229
Chromosome Location	chr5:58479300-58479301
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13160617	0.87[CEU][hapmap]
rs13164981	0.81[CEU][hapmap]
rs13180599	0.87[CEU][hapmap]
rs13185063	0.81[CEU][hapmap]
rs13185828	0.81[CEU][hapmap]
rs13186012	0.81[CEU][hapmap]
rs13361218	0.80[GIH][hapmap]
rs16877155	0.81[CEU][hapmap]
rs2059191	0.81[CEU][hapmap]
rs2409627	0.87[CEU][hapmap]
rs33950471	0.93[CEU][hapmap]
rs6450506	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs889229	LRRC70	cis	cerebellum	SCAN
rs889229	IPO11	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
2	chr5:58447600-58479600	Weak transcription	Left Ventricle	heart
3	chr5:58449800-58489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:58461000-58484200	Weak transcription	HUVEC	blood vessel
5	chr5:58464200-58484000	Weak transcription	Brain Anterior Caudate	brain
6	chr5:58464200-58485400	Weak transcription	Aorta	Aorta
7	chr5:58466200-58479400	Weak transcription	Psoas Muscle	Psoas
8	chr5:58469000-58483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:58469200-58484400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:58470000-58483400	Weak transcription	Fetal Lung	lung
11	chr5:58470200-58481400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:58470600-58480600	Weak transcription	Fetal Heart	heart
13	chr5:58470600-58482000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:58470600-58483800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:58471000-58483600	Weak transcription	Brain Angular Gyrus	brain
16	chr5:58471000-58483800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:58471000-58484800	Weak transcription	Pancreas	Pancrea
18	chr5:58471600-58484200	Weak transcription	Brain Germinal Matrix	brain
19	chr5:58472000-58484400	Weak transcription	Primary B cells from cord blood	blood
20	chr5:58472200-58485800	Weak transcription	Stomach Mucosa	stomach
21	chr5:58472400-58480800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:58472800-58484200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:58474400-58520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:58474600-58481200	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:58474600-58483600	Weak transcription	Fetal Brain Female	brain
26	chr5:58474600-58484400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr5:58474800-58481000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:58474800-58484400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:58474800-58484800	Weak transcription	Fetal Intestine Small	intestine
30	chr5:58474800-58491000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:58475000-58479600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:58475000-58484400	Weak transcription	Right Ventricle	heart
33	chr5:58475200-58484200	Weak transcription	Fetal Stomach	stomach
34	chr5:58475800-58484800	Weak transcription	Fetal Intestine Large	intestine
35	chr5:58476200-58479600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr5:58476400-58479600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:58476800-58484200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:58477600-58479800	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr5:58478400-58479400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr5:58478400-58479400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr5:58478400-58479400	Enhancers	HSMMtube	muscle
42	chr5:58478400-58479600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr5:58478400-58479800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr5:58478400-58480000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr5:58478400-58480000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr5:58478400-58481800	Genic enhancers	A549	lung
47	chr5:58478400-58483600	Weak transcription	Fetal Brain Male	brain
48	chr5:58478600-58479800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:58478600-58479800	Strong transcription	Fetal Muscle Leg	muscle
50	chr5:58478600-58480000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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