Variant report

Variant	rs9315683
Chromosome Location	chr13:39984967-39984968
allele	C/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:9)

rs_ID	r²[population]
rs17229842	0.82[YRI][hapmap]
rs17803662	1.00[ASW][hapmap]
rs9315682	1.00[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532376	0.85[JPT][hapmap]
rs9566424	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9566430	0.85[JPT][hapmap]
rs9576788	0.84[CEU][hapmap]
rs9576797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603532	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv900008	chr13:39962791-40020267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9315683	DGKH	cis	parietal	SCAN
rs9315683	LHFP	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39972800-39988600	Weak transcription	Fetal Muscle Leg	muscle
2	chr13:39975800-39988400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:39975800-39988600	Weak transcription	Right Atrium	heart
4	chr13:39976600-39990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr13:39977000-39987800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:39980200-39988600	Weak transcription	Fetal Stomach	stomach
7	chr13:39981400-39991800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:39981400-39991800	Weak transcription	NHEK	skin
9	chr13:39981600-39985200	Weak transcription	Ovary	ovary
10	chr13:39981800-39988600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr13:39982000-39986600	Enhancers	Fetal Heart	heart
12	chr13:39982400-39985200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:39983000-39985000	Enhancers	Right Ventricle	heart
14	chr13:39983200-39985600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr13:39983200-39986200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:39983200-39986600	Enhancers	Adipose Nuclei	Adipose
17	chr13:39983400-39989400	Weak transcription	Left Ventricle	heart
18	chr13:39983600-39985000	Enhancers	Brain Hippocampus Middle	brain
19	chr13:39983600-39985200	Enhancers	HUVEC	blood vessel
20	chr13:39983600-39986000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr13:39983600-39986000	Enhancers	Brain Anterior Caudate	brain
22	chr13:39983600-39986200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr13:39983600-39986600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr13:39983600-39986600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr13:39983600-39987200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr13:39983600-39987400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr13:39983800-39985000	Enhancers	Brain Substantia Nigra	brain
28	chr13:39983800-39985000	Enhancers	NHDF-Ad	bronchial
29	chr13:39983800-39985200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr13:39983800-39985200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr13:39983800-39985600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:39983800-39986000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr13:39983800-39986400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr13:39983800-39987200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:39984000-39985000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:39984200-39991200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr13:39984400-39985000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:39984400-39985000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr13:39984400-39985000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr13:39984400-39985800	Enhancers	Psoas Muscle	Psoas
41	chr13:39984400-39986000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr13:39984400-39986200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr13:39984400-39986200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr13:39984400-39986200	Enhancers	H9 Cell Line	embryonic stem cell
45	chr13:39984400-39986200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr13:39984400-39986400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr13:39984600-39985000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr13:39984600-39985000	Enhancers	HSMM	muscle
49	chr13:39984600-39986400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr13:39984600-39989000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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