Variant report

Variant	rs946780
Chromosome Location	chr10:99491715-99491716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99460906..99461905-chr10:99491204..99492125,3	K562	blood:
2	chr10:99460859..99461872-chr10:99491251..99492160,9	MCF-7	breast:
3	chr10:99468891..99470130-chr10:99490908..99491797,4	K562	blood:
4	chr10:99435936..99437099-chr10:99490664..99492104,9	K562	blood:
5	chr10:99467434..99470349-chr10:99491482..99494563,3	MCF-7	breast:
6	chr10:99473776..99476718-chr10:99490535..99492237,2	K562	blood:
7	chr10:99482033..99484147-chr10:99490073..99491810,2	MCF-7	breast:
8	chr10:99436228..99437666-chr10:99491411..99492160,6	MCF-7	breast:
9	chr10:99468809..99469891-chr10:99491266..99492143,11	MCF-7	breast:
10	chr10:99332125..99332702-chr10:99491238..99492185,4	K562	blood:
11	chr10:99466947..99470987-chr10:99489059..99494674,5	MCF-7	breast:
12	chr10:99488183..99489718-chr10:99490230..99493190,2	MCF-7	breast:
13	chr10:99473741..99475508-chr10:99489949..99491740,2	MCF-7	breast:
14	chr10:99471949..99474880-chr10:99491345..99493268,2	MCF-7	breast:
15	chr10:99469170..99469682-chr10:99491300..99492162,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155254	Chromatin interaction
ENSG00000165887	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10748707	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs10786368	0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10786369	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882992	0.82[AMR][1000 genomes]
rs1253023	0.96[AMR][1000 genomes];0.92[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];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4593946	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]
rs4917783	0.90[ASN][1000 genomes]
rs4917784	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs4919135	0.95[GIH][hapmap];0.81[MKK][hapmap]
rs6584149	0.82[GIH][hapmap]
rs7076831	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896853	0.82[GIH][hapmap]
rs946779	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs946780	PI4K2A	cis	parietal	SCAN
rs946780	MARVELD1	cis	lung	GTEx
rs946780	SEMA4G	cis	parietal	SCAN
rs946780	TLL2	cis	cerebellum	SCAN
rs946780	MARVELD1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99478800-99496400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:99486800-99496000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:99486800-99496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:99486800-99496400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:99486800-99496400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:99486800-99496400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:99486800-99496400	Weak transcription	Pancreas	Pancrea
8	chr10:99486800-99496600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:99487000-99491800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr10:99487000-99496000	Weak transcription	K562	blood
11	chr10:99487000-99496400	Weak transcription	Brain Anterior Caudate	brain
12	chr10:99487000-99496400	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:99487000-99496400	Weak transcription	A549	lung
14	chr10:99487200-99496400	Weak transcription	NHEK	skin
15	chr10:99487200-99496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:99487600-99496000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr10:99489200-99496200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr10:99491200-99491800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:99491200-99491800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:99491200-99492000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:99491200-99492000	Enhancers	Hela-S3	cervix
22	chr10:99491400-99491800	Enhancers	Brain Cingulate Gyrus	brain
23	chr10:99491400-99492000	Enhancers	HSMM	muscle
24	chr10:99491400-99492000	Enhancers	Osteobl	bone
25	chr10:99491600-99492000	Enhancers	HMEC	breast
26	chr10:99491600-99492000	Enhancers	HSMMtube	muscle
27	chr10:99491600-99496400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:99491600-99496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:99491600-99496400	Weak transcription	Brain Substantia Nigra	brain
30	chr10:99491600-99496400	Weak transcription	NHDF-Ad	bronchial
31	chr10:99491600-99496400	Weak transcription	NHLF	lung

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