Variant report

Variant	rs7908417
Chromosome Location	chr10:99278820-99278821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99275579..99277366-chr10:99277998..99279617,2	MCF-7	breast:
2	chr10:99278192..99281004-chr10:99284168..99285856,2	MCF-7	breast:
3	chr10:99272672..99275442-chr10:99278797..99280521,2	K562	blood:
4	chr10:99265449..99267822-chr10:99277534..99279101,2	K562	blood:
5	chr10:99275110..99276891-chr10:99277737..99279541,2	MCF-7	breast:
6	chr10:99275538..99279686-chr10:99333593..99336127,3	MCF-7	breast:
7	chr10:99257631..99259824-chr10:99278318..99280572,2	K562	blood:

Variant related genes	Relation type
ENSG00000155229	Chromatin interaction
ENSG00000165886	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10736118	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10748703	1.00[CHD][hapmap]
rs6584131	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs6584132	1.00[ASN][1000 genomes]
rs7071742	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077652	1.00[CHD][hapmap]
rs7097951	1.00[CHD][hapmap]
rs946985	0.89[AFR][1000 genomes];0.82[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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7908417	TCTN3	cis	cerebellum	SCAN
rs7908417	CC2D2B	cis	cerebellum	SCAN
rs7908417	CYP2C18	cis	cerebellum	SCAN
rs7908417	MORN4	cis	cerebellum	SCAN
rs7908417	C10orf12	cis	cerebellum	SCAN
rs7908417	FRAT2	cis	cerebellum	SCAN
rs7908417	KIAA0690	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99270800-99286200	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr10:99271200-99279200	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr10:99273800-99283200	Enhancers	Fetal Muscle Leg	muscle
4	chr10:99273800-99283200	Enhancers	Left Ventricle	heart
5	chr10:99274200-99279600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:99274200-99285000	Enhancers	Right Ventricle	heart
7	chr10:99274400-99280200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr10:99274600-99279800	Enhancers	Brain Substantia Nigra	brain
9	chr10:99274800-99279000	Enhancers	Fetal Muscle Trunk	muscle
10	chr10:99274800-99279400	Enhancers	Adipose Nuclei	Adipose
11	chr10:99275000-99293800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:99275400-99279000	Enhancers	Lung	lung
13	chr10:99276000-99284400	Weak transcription	HepG2	liver
14	chr10:99276600-99279000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:99276600-99279400	Enhancers	HMEC	breast
16	chr10:99276600-99279800	Enhancers	HUVEC	blood vessel
17	chr10:99276800-99279000	Enhancers	Fetal Stomach	stomach
18	chr10:99276800-99279600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:99276800-99279800	Enhancers	Brain Hippocampus Middle	brain
20	chr10:99276800-99280000	Enhancers	HSMM	muscle
21	chr10:99276800-99281400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr10:99277000-99279400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr10:99277000-99279600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr10:99277000-99279800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:99277000-99280400	Enhancers	Fetal Lung	lung
26	chr10:99277200-99279400	Enhancers	Brain Cingulate Gyrus	brain
27	chr10:99277200-99279800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr10:99277200-99282800	Enhancers	HSMMtube	muscle
29	chr10:99277400-99279200	Enhancers	Psoas Muscle	Psoas
30	chr10:99277400-99279400	Enhancers	Brain Anterior Caudate	brain
31	chr10:99277400-99279400	Enhancers	NH-A	brain
32	chr10:99277400-99279800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:99277400-99279800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:99277400-99279800	Enhancers	Brain Angular Gyrus	brain
35	chr10:99277400-99280000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr10:99277600-99279600	Enhancers	NHDF-Ad	bronchial
37	chr10:99277600-99279800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr10:99277800-99279400	Enhancers	NHLF	lung
39	chr10:99277800-99279600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr10:99277800-99279600	Enhancers	Osteobl	bone
41	chr10:99277800-99279800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:99277800-99281800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr10:99277800-99301800	Weak transcription	Gastric	stomach
44	chr10:99278000-99279800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr10:99278000-99279800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr10:99278000-99302600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr10:99278200-99279200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr10:99278200-99280400	Weak transcription	Pancreas	Pancrea
49	chr10:99278200-99281600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr10:99278200-99298800	Weak transcription	Aorta	Aorta

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