Variant report

Variant	rs4593946
Chromosome Location	chr10:99486644-99486645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99474184..99474793-chr10:99486201..99486865,2	Hela-S3	cervix:
2	chr10:99482956..99487048-chr10:99495082..99498802,5	MCF-7	breast:
3	chr10:99477505..99481349-chr10:99484055..99486700,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155254	Chromatin interaction
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10748707	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs10786368	0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10786369	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882992	0.84[AMR][1000 genomes]
rs12415272	0.83[LWK][hapmap];0.82[MKK][hapmap]
rs1253023	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253027	0.84[MEX][hapmap]
rs3818876	0.84[CEU][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4917783	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4917784	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs4919135	0.95[GIH][hapmap];0.89[LWK][hapmap];0.97[MKK][hapmap];0.86[YRI][hapmap]
rs6584148	0.86[MKK][hapmap]
rs6584149	0.82[GIH][hapmap];0.84[MKK][hapmap]
rs7076831	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896853	0.82[GIH][hapmap];0.85[MKK][hapmap]
rs7900119	0.86[YRI][hapmap]
rs7915100	0.86[YRI][hapmap]
rs946779	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs946780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4593946	MARVELD1	cis	lung	GTEx
rs4593946	MARVELD1	cis	Skin Sun Exposed Lower leg	GTEx
rs4593946	SEMA4G	cis	parietal	SCAN
rs4593946	PI4K2A	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99478800-99496400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:99479400-99491200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:99479600-99487000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:99484600-99488800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr10:99484800-99488600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr10:99484800-99488600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr10:99485800-99487000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr10:99486000-99486800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:99486000-99487600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr10:99486200-99486800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr10:99486200-99486800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:99486200-99486800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr10:99486200-99486800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr10:99486200-99486800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:99486200-99486800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:99486200-99486800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr10:99486200-99486800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:99486200-99486800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:99486200-99486800	Enhancers	Fetal Intestine Large	intestine
20	chr10:99486200-99486800	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr10:99486400-99486800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr10:99486400-99486800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr10:99486400-99486800	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr10:99486400-99486800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr10:99486400-99486800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:99486400-99486800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr10:99486400-99486800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr10:99486400-99486800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr10:99486400-99486800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:99486400-99486800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:99486400-99486800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr10:99486400-99486800	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr10:99486400-99486800	Enhancers	Liver	Liver
34	chr10:99486400-99486800	Active TSS	Brain Cingulate Gyrus	brain
35	chr10:99486400-99486800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr10:99486400-99486800	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr10:99486400-99486800	Flanking Active TSS	Colonic Mucosa	Colon
38	chr10:99486400-99486800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr10:99486400-99486800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr10:99486400-99486800	Flanking Active TSS	Fetal Heart	heart
41	chr10:99486400-99486800	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr10:99486400-99486800	Flanking Active TSS	Fetal Lung	lung
43	chr10:99486400-99486800	Enhancers	Fetal Muscle Leg	muscle
44	chr10:99486400-99486800	Enhancers	Placenta	Placenta
45	chr10:99486400-99486800	Enhancers	Left Ventricle	heart
46	chr10:99486400-99486800	Enhancers	Pancreas	Pancrea
47	chr10:99486400-99486800	Active TSS	Psoas Muscle	Psoas
48	chr10:99486400-99486800	Enhancers	Right Ventricle	heart
49	chr10:99486400-99486800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr10:99486400-99486800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links