Variant report

Variant	rs10121424
Chromosome Location	chr9:116800606-116800607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10124293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759679	0.92[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs10982028	0.85[EUR][1000 genomes]
rs10982035	0.88[CEU][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes]
rs10982040	0.91[EUR][1000 genomes]
rs10982041	0.92[EUR][1000 genomes]
rs11793049	0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs13297916	0.88[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs17793015	0.86[EUR][1000 genomes]
rs2418264	0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35794395	0.86[EUR][1000 genomes]
rs4574916	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs4979333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752035	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs7863836	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10121424	SLC31A2	cis	cerebellum	SCAN
rs10121424	DEC1	cis	parietal	SCAN
rs10121424	HSDL2	cis	parietal	SCAN
rs10121424	ZNF483	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116766600-116811200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:116773600-116809200	Weak transcription	Fetal Heart	heart
3	chr9:116785200-116811200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:116785400-116810600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:116787000-116803000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:116787000-116812800	Weak transcription	Primary B cells from cord blood	blood
7	chr9:116788000-116802400	Strong transcription	Adipose Nuclei	Adipose
8	chr9:116789600-116808600	Weak transcription	HMEC	breast
9	chr9:116790600-116801400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:116790600-116801600	Strong transcription	Spleen	Spleen
11	chr9:116790600-116802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:116790600-116802600	Strong transcription	Liver	Liver
13	chr9:116792200-116802800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:116792200-116810400	Weak transcription	Thymus	Thymus
15	chr9:116792400-116801600	Strong transcription	HUVEC	blood vessel
16	chr9:116793000-116802600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:116793200-116811200	Weak transcription	Stomach Mucosa	stomach
18	chr9:116793200-116812200	Weak transcription	K562	blood
19	chr9:116793200-116813800	Weak transcription	NHEK	skin
20	chr9:116794000-116802400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:116794200-116800800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:116794200-116801600	Strong transcription	Pancreas	Pancrea
23	chr9:116794600-116801400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:116795000-116801600	Strong transcription	Fetal Intestine Large	intestine
25	chr9:116795200-116802600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:116795200-116821800	Weak transcription	Right Atrium	heart
27	chr9:116795600-116802400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:116795800-116801600	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:116796000-116802600	Strong transcription	A549	lung
30	chr9:116796000-116802800	Strong transcription	Fetal Lung	lung
31	chr9:116796200-116815800	Weak transcription	Small Intestine	intestine
32	chr9:116796400-116801200	Weak transcription	NHDF-Ad	bronchial
33	chr9:116796800-116802800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:116797200-116802200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:116797800-116802600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr9:116798000-116800800	Strong transcription	Gastric	stomach
37	chr9:116798000-116802400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr9:116798000-116802400	Strong transcription	NH-A	brain
39	chr9:116798000-116802600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:116798000-116802600	Strong transcription	Ovary	ovary
41	chr9:116798000-116802800	Strong transcription	Fetal Muscle Leg	muscle
42	chr9:116798200-116801000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:116798400-116801000	Strong transcription	Left Ventricle	heart
44	chr9:116798400-116802600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:116798400-116802600	Strong transcription	Osteobl	bone
46	chr9:116798800-116801600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:116799000-116800800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr9:116799000-116801000	Strong transcription	Aorta	Aorta
49	chr9:116799000-116801600	Strong transcription	Rectal Smooth Muscle	rectum
50	chr9:116799000-116811200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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