Variant report

Variant	rs7896853
Chromosome Location	chr10:99476915-99476916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99443080..99453237-chr10:99471420..99478243,12	MCF-7	breast:
2	chr10:99472128..99477527-chr10:99495091..99498402,11	MCF-7	breast:
3	chr10:99444102..99447131-chr10:99475724..99478855,3	MCF-7	breast:
4	chr10:99476839..99480454-chr10:99481730..99484335,3	K562	blood:
5	chr10:99476464..99480454-chr10:99480682..99484335,5	K562	blood:

Variant related genes	Relation type
ENSG00000119986	Chromatin interaction
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10748706	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189342	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12415272	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4593946	0.82[GIH][hapmap];0.85[MKK][hapmap]
rs4919133	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4919135	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6584148	0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6584149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7900119	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7914697	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7915100	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs946780	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7896853	C10orf62	cis	cerebellum	SCAN
rs7896853	MARVELD1	cis	lung	GTEx
rs7896853	MARVELD1	cis	Thyroid	GTEx
rs7896853	SEMA4G	cis	parietal	SCAN
rs7896853	MARVELD1	cis	Skin Sun Exposed Lower leg	GTEx
rs7896853	PI4K2A	cis	parietal	SCAN
rs7896853	FBXW4	cis	parietal	SCAN
rs7896853	DHDPSL	cis	cerebellum	SCAN
rs7896853	ZFYVE27	cis	cerebellum	SCAN
rs7896853	TLL2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99473800-99479000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr10:99474400-99477800	Weak transcription	Liver	Liver
3	chr10:99474800-99477400	Weak transcription	Gastric	stomach
4	chr10:99474800-99478000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr10:99474800-99478000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:99475000-99477000	Enhancers	Fetal Heart	heart
7	chr10:99475000-99477200	Weak transcription	Brain Angular Gyrus	brain
8	chr10:99475000-99478000	Weak transcription	Small Intestine	intestine
9	chr10:99475000-99479400	Weak transcription	Fetal Kidney	kidney
10	chr10:99475200-99477000	Weak transcription	Left Ventricle	heart
11	chr10:99475200-99477000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr10:99475200-99477200	Weak transcription	Brain Substantia Nigra	brain
13	chr10:99475200-99477200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr10:99475200-99477400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:99475200-99477400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr10:99475200-99477400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:99475200-99477600	Weak transcription	Lung	lung
18	chr10:99475200-99478000	Weak transcription	Right Ventricle	heart
19	chr10:99475200-99478200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:99475200-99478200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr10:99475200-99478200	Weak transcription	Pancreas	Pancrea
22	chr10:99475400-99477000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
23	chr10:99475400-99477400	Weak transcription	Spleen	Spleen
24	chr10:99475400-99478000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr10:99475400-99478000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:99475400-99478000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr10:99475600-99477000	Weak transcription	Placenta	Placenta
28	chr10:99475600-99477200	Weak transcription	K562	blood
29	chr10:99475600-99477400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr10:99475600-99477400	Transcr. at gene 5' and 3'	Hela-S3	cervix
31	chr10:99475800-99477000	Weak transcription	Brain Anterior Caudate	brain
32	chr10:99475800-99477000	Weak transcription	Colonic Mucosa	Colon
33	chr10:99475800-99477200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr10:99475800-99477400	Weak transcription	Esophagus	oesophagus
35	chr10:99475800-99477400	Strong transcription	Fetal Intestine Large	intestine
36	chr10:99475800-99477400	Strong transcription	Fetal Intestine Small	intestine
37	chr10:99475800-99478800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr10:99475800-99479200	Genic enhancers	Colon Smooth Muscle	Colon
39	chr10:99476000-99477000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
40	chr10:99476000-99477200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:99476000-99478000	Genic enhancers	A549	lung
42	chr10:99476000-99478400	Weak transcription	HSMMtube	muscle
43	chr10:99476000-99478800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:99476000-99479600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:99476000-99479600	Genic enhancers	Fetal Muscle Leg	muscle
46	chr10:99476000-99479600	Genic enhancers	Fetal Stomach	stomach
47	chr10:99476200-99477200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr10:99476200-99477400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:99476200-99477600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr10:99476200-99477600	Weak transcription	Brain Germinal Matrix	brain

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