Variant report

Variant	rs10739968
Chromosome Location	chr9:96849137-96849138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96845151..96851769-chr9:96927067..96931565,10	K562	blood:
2	chr9:96847188..96849533-chr9:96856467..96859477,3	K562	blood:
3	chr9:96848027..96849533-chr9:96856014..96858976,2	K562	blood:
4	chr9:96845151..96850974-chr9:96927067..96931575,8	K562	blood:
5	chr9:96793114..96795953-chr9:96849084..96851331,2	K562	blood:
6	chr9:96848883..96850819-chr9:96911987..96913565,2	MCF-7	breast:
7	chr9:96847639..96850039-chr9:96863471..96865147,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1756962	0.84[ASN][1000 genomes]
rs1819445	0.86[ASN][1000 genomes]
rs1890383	0.84[ASN][1000 genomes]
rs2150624	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3858083	0.86[EUR][1000 genomes];0.93[ASN][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	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
3	nsv1043704	chr9:96816552-96873018	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
5	nsv893591	chr9:96849137-96883271	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10739968	C10orf79	trans	cerebellum	SCAN
rs10739968	CKS2	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96822400-96859800	Weak transcription	Psoas Muscle	Psoas
2	chr9:96824200-96860000	Weak transcription	Aorta	Aorta
3	chr9:96824200-96869600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:96824400-96850000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:96828200-96859600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:96828200-96860800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr9:96828200-96862000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:96828200-96868200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:96829600-96872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:96832000-96859800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:96834400-96859800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:96835400-96861800	Weak transcription	Primary B cells from cord blood	blood
13	chr9:96837000-96857400	Weak transcription	HSMM	muscle
14	chr9:96837200-96857400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr9:96837200-96858600	Weak transcription	Dnd41	blood
16	chr9:96837200-96859800	Weak transcription	Fetal Intestine Small	intestine
17	chr9:96837400-96850600	Weak transcription	Adipose Nuclei	Adipose
18	chr9:96837400-96860200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:96837600-96859200	Weak transcription	Primary T cells from cord blood	blood
20	chr9:96840200-96863600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:96840400-96850000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:96842600-96858200	Weak transcription	HSMMtube	muscle
23	chr9:96843600-96857000	Weak transcription	Colonic Mucosa	Colon
24	chr9:96845000-96853400	Weak transcription	GM12878-XiMat	blood
25	chr9:96845200-96857600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:96845600-96858200	Weak transcription	Right Ventricle	heart
27	chr9:96845600-96858400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:96845600-96885400	Weak transcription	Gastric	stomach
29	chr9:96846000-96870600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:96846200-96859800	Weak transcription	Ovary	ovary
31	chr9:96846800-96849400	Enhancers	NH-A	brain
32	chr9:96847000-96850400	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:96847000-96857000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:96847000-96859000	Weak transcription	Lung	lung
35	chr9:96847000-96859800	Weak transcription	Pancreas	Pancrea
36	chr9:96847000-96860200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:96847200-96859000	Weak transcription	Fetal Brain Male	brain
38	chr9:96847200-96859000	Weak transcription	Fetal Brain Female	brain
39	chr9:96847400-96849400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr9:96847400-96849400	Enhancers	Osteobl	bone
41	chr9:96847400-96850200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:96847600-96849600	Enhancers	NHEK	skin
43	chr9:96847600-96850000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:96847600-96856800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr9:96847600-96859200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:96847800-96849200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr9:96847800-96849400	Enhancers	Brain Angular Gyrus	brain
48	chr9:96847800-96849800	Enhancers	Brain Hippocampus Middle	brain
49	chr9:96847800-96850000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:96847800-96850200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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