Variant report

Variant	rs10119350
Chromosome Location	chr9:6496811-6496812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6412621..6414719-chr9:6496485..6499094,2	K562	blood:

Variant related genes	Relation type
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10739104	1.00[JPT][hapmap]
rs1156869	1.00[JPT][hapmap]
rs13283464	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13283631	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13283687	0.84[EUR][1000 genomes]
rs13284032	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13285035	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13285125	0.96[EUR][1000 genomes]
rs13285152	0.84[EUR][1000 genomes]
rs13285458	0.84[EUR][1000 genomes]
rs13285949	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13286720	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13288875	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13290027	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13290126	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13290488	0.96[EUR][1000 genomes]
rs13291494	0.84[EUR][1000 genomes]
rs13291887	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13292030	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs13294924	0.96[EUR][1000 genomes]
rs13296481	0.84[EUR][1000 genomes]
rs13296692	0.96[EUR][1000 genomes]
rs13299896	0.84[EUR][1000 genomes]
rs13300059	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13302032	0.84[EUR][1000 genomes]
rs1563	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs34529113	0.91[EUR][1000 genomes]
rs34530211	0.84[EUR][1000 genomes]
rs34581400	0.84[EUR][1000 genomes]
rs34905133	0.91[EUR][1000 genomes]
rs35301257	0.84[EUR][1000 genomes]
rs35408061	0.84[EUR][1000 genomes]
rs36089474	0.84[EUR][1000 genomes]
rs4742198	1.00[JPT][hapmap]
rs553048	0.84[EUR][1000 genomes]
rs67797327	0.96[EUR][1000 genomes]
rs7043824	1.00[JPT][hapmap]
rs72693587	0.84[EUR][1000 genomes]
rs7869419	0.84[EUR][1000 genomes]
rs7872349	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7875172	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv892162	chr9:6480005-6788085	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
13	esv3363138	chr9:6493894-6497217	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
14	nsv831498	chr9:6496021-6689728	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10119350	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6458800-6497200	Weak transcription	Colonic Mucosa	Colon
2	chr9:6459400-6501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
4	chr9:6467400-6497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:6471600-6501800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:6471600-6504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:6472200-6497200	Weak transcription	Aorta	Aorta
8	chr9:6472200-6508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:6473000-6499600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:6473800-6498400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:6473800-6506200	Weak transcription	Small Intestine	intestine
12	chr9:6474800-6502800	Strong transcription	Dnd41	blood
13	chr9:6475200-6503000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:6475400-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:6475400-6508400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:6475400-6508800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr9:6475400-6508800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr9:6475800-6497200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:6475800-6509000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:6475800-6510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:6476000-6509400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:6477600-6497800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:6477600-6507800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:6477800-6511000	Weak transcription	Fetal Heart	heart
25	chr9:6478000-6498200	Weak transcription	Brain Angular Gyrus	brain
26	chr9:6478200-6498000	Weak transcription	Esophagus	oesophagus
27	chr9:6478400-6503400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr9:6478600-6498600	Weak transcription	Spleen	Spleen
29	chr9:6480200-6508400	Weak transcription	Stomach Mucosa	stomach
30	chr9:6480400-6497400	Weak transcription	Psoas Muscle	Psoas
31	chr9:6481600-6502800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr9:6483200-6498000	Strong transcription	HMEC	breast
33	chr9:6484000-6498600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:6484400-6498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:6484600-6497800	Weak transcription	Pancreas	Pancrea
36	chr9:6484600-6501800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:6485800-6498000	Weak transcription	Gastric	stomach
38	chr9:6487000-6497200	Weak transcription	Brain Substantia Nigra	brain
39	chr9:6487000-6497200	Weak transcription	K562	blood
40	chr9:6487600-6497200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:6487600-6497200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:6487600-6498000	Weak transcription	Brain Anterior Caudate	brain
43	chr9:6487600-6499600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr9:6487600-6510600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr9:6488000-6497600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:6488200-6497000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr9:6488200-6497200	Weak transcription	Ovary	ovary
48	chr9:6488200-6497800	Weak transcription	Brain Germinal Matrix	brain
49	chr9:6488200-6497800	Weak transcription	Lung	lung
50	chr9:6488200-6497800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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