Variant report

Variant	rs3818876
Chromosome Location	chr10:99498234-99498235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr10:99497884-99498474	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:99496268-99498505	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:99498234-99498487	HepG2	liver:	n/a	n/a
4	POLR2A	chr10:99498222-99498240	K562	blood:	n/a	n/a
5	POLR2A	chr10:99498185-99498664	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99446145..99449629-chr10:99495749..99499452,3	K562	blood:
2	chr10:99496214..99498358-chr10:99509556..99512391,2	K562	blood:
3	chr10:99472472..99476089-chr10:99494153..99498366,9	MCF-7	breast:
4	chr10:99472128..99477527-chr10:99495091..99498402,11	MCF-7	breast:
5	chr10:99446264..99449966-chr10:99495266..99498485,3	MCF-7	breast:
6	chr10:99496988..99498940-chr10:99509067..99511500,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZFYVE27	TF binding region
ENSG00000155254	Chromatin interaction
ENSG00000119986	Chromatin interaction
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10748707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10786368	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253023	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3829137	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs4593946	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	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4917784	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4917785	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4919135	0.91[YRI][hapmap]
rs7076831	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7900119	0.91[YRI][hapmap]
rs7915100	0.91[YRI][hapmap]
rs946779	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs946780	0.84[CEU][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3818876	MARVELD1	cis	lung	GTEx
rs3818876	SEMA4G	cis	parietal	SCAN
rs3818876	LZTS2	cis	cerebellum	SCAN
rs3818876	ZFYVE27	cis	parietal	SCAN
rs3818876	FBXW4	cis	parietal	SCAN
rs3818876	MARVELD1	cis	Thyroid	GTEx
rs3818876	TLL2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99496400-99498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:99496800-99498600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:99497200-99498400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr10:99497200-99498400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr10:99497200-99498600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:99497200-99498600	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr10:99497400-99498400	Flanking Active TSS	Right Ventricle	heart
8	chr10:99497400-99498600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr10:99497400-99498600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr10:99497400-99498600	Flanking Active TSS	Rectal Smooth Muscle	rectum
11	chr10:99497600-99498400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr10:99497600-99498400	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr10:99497600-99498400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:99497600-99498400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:99497600-99498400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr10:99497600-99498400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:99497600-99498400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:99497600-99498400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:99497600-99498400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr10:99497600-99498400	Flanking Active TSS	Spleen	Spleen
21	chr10:99497600-99498400	Flanking Active TSS	HSMMtube	muscle
22	chr10:99497600-99498400	Flanking Active TSS	NHLF	lung
23	chr10:99497600-99498400	Flanking Active TSS	Osteobl	bone
24	chr10:99497600-99498600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:99497600-99498600	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr10:99497600-99498600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
27	chr10:99497600-99498600	Flanking Active TSS	Hela-S3	cervix
28	chr10:99497600-99498600	Flanking Active TSS	K562	blood
29	chr10:99497600-99522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr10:99497800-99498400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:99497800-99498400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:99497800-99498400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr10:99497800-99498400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr10:99497800-99498400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr10:99497800-99498400	Enhancers	Small Intestine	intestine
36	chr10:99497800-99498400	Flanking Active TSS	HMEC	breast
37	chr10:99497800-99498600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:99497800-99498600	Enhancers	Fetal Heart	heart
39	chr10:99497800-99498600	Enhancers	Placenta	Placenta
40	chr10:99497800-99498600	Flanking Active TSS	Gastric	stomach
41	chr10:99497800-99498800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr10:99498000-99498400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:99498000-99498400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr10:99498000-99498400	Enhancers	Primary B cells from cord blood	blood
45	chr10:99498000-99498400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr10:99498000-99498400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr10:99498000-99498400	Genic enhancers	Fetal Stomach	stomach
48	chr10:99498000-99498400	Enhancers	Stomach Mucosa	stomach
49	chr10:99498000-99498400	Flanking Active TSS	HepG2	liver
50	chr10:99498000-99498400	Enhancers	NH-A	brain

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