Variant report

Variant	rs9314990
Chromosome Location	chr13:30517787-30517788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11841228	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1359475	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4318068	0.82[AMR][1000 genomes]
rs4769779	0.82[AMR][1000 genomes]
rs4769780	0.82[AMR][1000 genomes]
rs4769781	0.85[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs512583	0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs566495	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs576712	0.80[ASN][1000 genomes]
rs634413	0.89[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs646917	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6490436	0.82[ASN][1000 genomes]
rs6490437	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7322038	0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs7332851	0.83[ASN][1000 genomes]
rs7334559	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7334714	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7339208	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7994222	0.87[MEX][hapmap]
rs912788	0.83[CEU][hapmap]
rs9314991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314992	0.85[EUR][1000 genomes]
rs9506244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508594	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9314990	SH3BGRL2	trans	cerebellum	SCAN
rs9314990	FLT1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30510800-30521600	Weak transcription	Pancreas	Pancrea
2	chr13:30512400-30518400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr13:30514000-30518000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr13:30514000-30522600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:30515200-30518000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr13:30515800-30517800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr13:30516400-30518600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:30516400-30518800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr13:30516600-30518200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr13:30516600-30518600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr13:30516600-30518600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr13:30516600-30518800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr13:30516600-30519000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr13:30516800-30518400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr13:30516800-30518400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr13:30516800-30518600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr13:30517000-30518600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr13:30517200-30517800	Enhancers	Primary T cells from cord blood	blood
19	chr13:30517200-30518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr13:30517200-30518200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:30517200-30518200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr13:30517200-30518400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:30517200-30518400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr13:30517400-30517800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:30517400-30517800	Enhancers	Brain Germinal Matrix	brain
26	chr13:30517400-30518200	Enhancers	Stomach Mucosa	stomach
27	chr13:30517400-30526000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr13:30517600-30517800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr13:30517600-30518200	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr13:30517600-30518400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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