Variant report

Variant	rs10882299
Chromosome Location	chr10:95438964-95438965
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr10:95438227-95439120	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr10:95438633-95439089	SH-SY5Y	brain:	n/a	chr10:95438790-95438811 chr10:95438797-95438804 chr10:95438797-95438804 chr10:95438797-95438804
3	REST	chr10:95438759-95439621	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:95429639..95431834-chr10:95437485..95439775,2	MCF-7	breast:
2	chr10:95434915..95436614-chr10:95438819..95440992,2	MCF-7	breast:

Variant related genes	Relation type
FRA10AC1	TF binding region
ENSG00000148690	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10444062	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10882302	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882303	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187583	0.81[CEU][hapmap];0.84[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187584	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187585	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187596	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11187599	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11187620	0.86[ASN][1000 genomes]
rs1998840	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs45468996	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094280	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047261	chr10:95384527-95449653	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv540746	chr10:95384527-95449653	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1050705	chr10:95384527-95469255	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv540747	chr10:95384527-95469255	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv3346948	chr10:95421957-95532625	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10882299	NUDT9P1	cis	parietal	SCAN
rs10882299	FRA10AC1	cis	parietal	SCAN
rs10882299	FRA10AC1	cis	Artery Tibial	GTEx
rs10882299	CYP2C8	cis	parietal	SCAN
rs10882299	FRA10AC1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95416600-95453800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:95417800-95461400	Weak transcription	Esophagus	oesophagus
3	chr10:95418400-95461400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr10:95418600-95460800	Weak transcription	Aorta	Aorta
5	chr10:95418600-95462000	Weak transcription	Spleen	Spleen
6	chr10:95418800-95451600	Weak transcription	Hela-S3	cervix
7	chr10:95419400-95445400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr10:95420400-95458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:95421400-95439000	Weak transcription	Fetal Heart	heart
10	chr10:95421600-95453600	Weak transcription	Pancreas	Pancrea
11	chr10:95422200-95451000	Weak transcription	Right Ventricle	heart
12	chr10:95422600-95440400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:95422800-95441800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:95424600-95456600	Weak transcription	Fetal Intestine Small	intestine
15	chr10:95424800-95441200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:95424800-95453400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr10:95425000-95441600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:95425000-95446000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr10:95425200-95461400	Weak transcription	K562	blood
20	chr10:95425600-95440800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr10:95425600-95441400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr10:95426000-95461400	Weak transcription	Colonic Mucosa	Colon
23	chr10:95426600-95440000	Strong transcription	Osteobl	bone
24	chr10:95426800-95441200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr10:95426800-95441200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr10:95427400-95456600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr10:95428600-95439200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:95428600-95444400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr10:95428800-95440800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:95428800-95455400	Weak transcription	Brain Angular Gyrus	brain
31	chr10:95429000-95460600	Weak transcription	Small Intestine	intestine
32	chr10:95429200-95455000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr10:95430600-95451400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr10:95430600-95456600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr10:95430600-95461200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:95431800-95439600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr10:95432000-95441200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr10:95432000-95441200	Strong transcription	NH-A	brain
39	chr10:95432000-95445600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr10:95432400-95441000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr10:95432400-95441200	Strong transcription	Placenta	Placenta
42	chr10:95432400-95461200	Weak transcription	Stomach Mucosa	stomach
43	chr10:95432600-95439600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr10:95432600-95439800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr10:95432600-95440800	Strong transcription	Fetal Lung	lung
46	chr10:95432600-95441000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr10:95432600-95442400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:95432800-95439600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr10:95432800-95440000	Strong transcription	Adipose Nuclei	Adipose
50	chr10:95432800-95441000	Strong transcription	Dnd41	blood

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