Variant report

Variant	rs4919135
Chromosome Location	chr10:99484628-99484629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99482956..99487048-chr10:99495082..99498802,5	MCF-7	breast:
2	chr10:99442496..99444028-chr10:99483468..99485995,2	MCF-7	breast:
3	chr10:99445462..99447527-chr10:99483205..99486633,3	MCF-7	breast:
4	chr10:99477505..99481349-chr10:99484055..99486700,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119986	Chromatin interaction
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10748706	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10786368	0.91[YRI][hapmap]
rs11189342	0.82[ASN][1000 genomes]
rs12415272	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1253027	0.85[CEU][hapmap]
rs3818876	0.91[YRI][hapmap]
rs4593946	0.95[GIH][hapmap];0.89[LWK][hapmap];0.97[MKK][hapmap];0.86[YRI][hapmap]
rs4919133	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6584148	0.90[CHB][hapmap];0.89[CHD][hapmap];0.86[MKK][hapmap]
rs6584149	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7896853	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]
rs7900119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7914697	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7915100	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs946779	0.95[YRI][hapmap]
rs946780	0.95[GIH][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv519864	chr10:99478081-99486644	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4919135	MARVELD1	cis	Thyroid	GTEx
rs4919135	TLL2	cis	cerebellum	SCAN
rs4919135	SEMA4G	cis	parietal	SCAN
rs4919135	MARVELD1	cis	Skin Sun Exposed Lower leg	GTEx
rs4919135	PI4K2A	cis	parietal	SCAN
rs4919135	C10orf62	cis	cerebellum	SCAN
rs4919135	C10orf12	cis	cerebellum	SCAN
rs4919135	FBXW4	cis	parietal	SCAN
rs4919135	MARVELD1	cis	lung	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99476200-99486600	Weak transcription	Ovary	ovary
2	chr10:99476600-99486200	Weak transcription	HUVEC	blood vessel
3	chr10:99477200-99486200	Weak transcription	NH-A	brain
4	chr10:99478400-99486400	Weak transcription	Aorta	Aorta
5	chr10:99478800-99486600	Weak transcription	HSMMtube	muscle
6	chr10:99478800-99496400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:99479000-99486200	Weak transcription	Fetal Heart	heart
8	chr10:99479200-99486200	Weak transcription	Adipose Nuclei	Adipose
9	chr10:99479200-99486400	Weak transcription	Liver	Liver
10	chr10:99479400-99491200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:99479600-99486200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:99479600-99486200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:99479600-99486200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:99479600-99486400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:99479600-99486400	Weak transcription	Brain Substantia Nigra	brain
16	chr10:99479600-99486400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr10:99479600-99486400	Weak transcription	Fetal Lung	lung
18	chr10:99479600-99486400	Weak transcription	Fetal Muscle Leg	muscle
19	chr10:99479600-99486400	Weak transcription	HSMM	muscle
20	chr10:99479600-99487000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:99479800-99486200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr10:99479800-99486200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr10:99479800-99486200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr10:99479800-99486200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:99479800-99486200	Weak transcription	Colon Smooth Muscle	Colon
26	chr10:99479800-99486200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr10:99481600-99486600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr10:99481800-99484800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr10:99482400-99486400	Weak transcription	Fetal Intestine Small	intestine
30	chr10:99482400-99486400	Weak transcription	Stomach Mucosa	stomach
31	chr10:99482600-99486200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:99482800-99484800	Enhancers	NHEK	skin
33	chr10:99482800-99486400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr10:99483000-99486000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr10:99483000-99486400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:99483000-99486400	Weak transcription	Fetal Stomach	stomach
37	chr10:99483200-99486400	Weak transcription	Placenta	Placenta
38	chr10:99483600-99484800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:99483800-99484800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr10:99483800-99484800	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr10:99483800-99485400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr10:99484000-99484800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:99484000-99484800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:99484000-99484800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr10:99484000-99484800	Enhancers	K562	blood
46	chr10:99484000-99484800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr10:99484000-99484800	Enhancers	NHDF-Ad	bronchial
48	chr10:99484000-99485000	Enhancers	Hela-S3	cervix
49	chr10:99484200-99484800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr10:99484200-99486400	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links