Variant report

Variant	rs1870077
Chromosome Location	chr5:58834852-58834853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17796824	0.88[MKK][hapmap]
rs34660223	0.80[AMR][1000 genomes]
rs72769711	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1870077	SLC38A9	cis	parietal	SCAN
rs1870077	PDE4D	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58822200-58838800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:58822800-58837600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58823000-58838200	Weak transcription	Fetal Brain Male	brain
4	chr5:58824800-58836000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:58825000-58838600	Weak transcription	HSMMtube	muscle
6	chr5:58828200-58836200	Genic enhancers	A549	lung
7	chr5:58828800-58838800	Weak transcription	Gastric	stomach
8	chr5:58830400-58839000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:58831800-58836000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:58833200-58835800	Weak transcription	Stomach Mucosa	stomach
11	chr5:58834200-58835000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr5:58834600-58835000	Enhancers	Colon Smooth Muscle	Colon
13	chr5:58834600-58838800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:58834600-58840600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr5:58834600-58840800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:58834800-58835400	Weak transcription	Brain Germinal Matrix	brain
17	chr5:58834800-58835600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:58834800-58835800	Weak transcription	Brain Anterior Caudate	brain
19	chr5:58834800-58835800	Weak transcription	Psoas Muscle	Psoas
20	chr5:58834800-58836200	Weak transcription	Rectal Smooth Muscle	rectum

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