Variant report

Variant	rs10787286
Chromosome Location	chr10:112623274-112623275
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:112619976..112621835-chr10:112622055..112625024,2	MCF-7	breast:
2	chr10:112589697..112592145-chr10:112622610..112625288,3	MCF-7	breast:
3	chr10:112621767..112623354-chr10:112678142..112681449,3	K562	blood:

Variant related genes	Relation type
ENSG00000108061	Chromatin interaction
ENSG00000214413	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10082499	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10787291	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10787293	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10885059	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885060	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885061	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10885064	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10885071	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10885076	0.80[CEU][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs11195361	0.84[ASN][1000 genomes]
rs11195366	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11195381	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11195387	0.80[CEU][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11195390	0.80[CEU][hapmap];0.92[AFR][1000 genomes]
rs11195391	1.00[JPT][hapmap]
rs11195398	0.80[CEU][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12240685	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12242177	0.84[AFR][1000 genomes]
rs12242928	0.84[AFR][1000 genomes]
rs12246561	0.81[AFR][1000 genomes]
rs12249031	0.81[AFR][1000 genomes]
rs12256157	1.00[CHB][hapmap]
rs12258559	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12261765	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12572941	1.00[CHB][hapmap]
rs12776359	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12776861	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12783690	1.00[JPT][hapmap]
rs2146544	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.80[AFR][1000 genomes]
rs34401279	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34893229	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35394459	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35793075	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35946882	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750619	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3763692	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917589	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6585026	0.80[CEU][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs7074629	0.81[AFR][1000 genomes]
rs7089687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[TSI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096359	0.81[AFR][1000 genomes]
rs7919142	1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.80[AFR][1000 genomes]
rs9663346	0.80[AFR][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	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10787286	LOC92482	Cis_1M	lymphoblastoid	RTeQTL
rs10787286	HABP2	cis	parietal	SCAN
rs10787286	XPNPEP1	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112611200-112630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:112614800-112624400	Weak transcription	Aorta	Aorta
3	chr10:112617000-112624200	Enhancers	Primary hematopoietic stem cells	blood
4	chr10:112617000-112624600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr10:112617000-112624600	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:112617000-112624600	Enhancers	Primary T cells fromperipheralblood	blood
7	chr10:112617000-112624600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:112617000-112628600	Enhancers	Placenta	Placenta
9	chr10:112617200-112624400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:112617400-112624200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:112617400-112624200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr10:112617800-112630600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:112618000-112624600	Weak transcription	Left Ventricle	heart
14	chr10:112618400-112630800	Enhancers	Fetal Thymus	thymus
15	chr10:112618600-112623800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:112618600-112624000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:112618600-112624400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr10:112618600-112624600	Enhancers	Duodenum Mucosa	Duodenum
19	chr10:112619400-112623800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:112619400-112624800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr10:112619800-112624200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr10:112619800-112624200	Enhancers	Thymus	Thymus
23	chr10:112619800-112624400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr10:112619800-112624400	Weak transcription	Brain Angular Gyrus	brain
25	chr10:112619800-112627400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr10:112620000-112623800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr10:112620000-112624600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr10:112620000-112624600	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:112620000-112624800	Weak transcription	Psoas Muscle	Psoas
30	chr10:112620200-112623400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:112620200-112623600	Weak transcription	HSMM	muscle
32	chr10:112620200-112624400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:112620200-112624600	Enhancers	NHEK	skin
34	chr10:112620400-112623600	Weak transcription	Brain Anterior Caudate	brain
35	chr10:112620400-112624400	Weak transcription	Osteobl	bone
36	chr10:112620400-112624600	Weak transcription	Colon Smooth Muscle	Colon
37	chr10:112620600-112623600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:112620600-112623800	Weak transcription	Fetal Lung	lung
39	chr10:112620600-112623800	Weak transcription	Hela-S3	cervix
40	chr10:112620600-112624400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr10:112620600-112624400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr10:112620600-112624400	Weak transcription	NHLF	lung
43	chr10:112620600-112624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr10:112620800-112624400	Weak transcription	Dnd41	blood
45	chr10:112621000-112623600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr10:112621000-112623600	Weak transcription	Lung	lung
47	chr10:112621000-112623800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr10:112621000-112623800	Weak transcription	Right Atrium	heart
49	chr10:112621000-112624200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr10:112621000-112624400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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