Variant report

Variant	rs10984811
Chromosome Location	chr9:100784050-100784051
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100784033..100788653-chr9:100792674..100797277,7	K562	blood:
2	chr9:100774780..100779950-chr9:100780337..100785356,9	K562	blood:

Variant related genes	Relation type
ENSG00000212521	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10081625	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs10081626	0.93[EUR][1000 genomes]
rs10283632	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10283737	1.00[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10984650	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10984775	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984822	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10984829	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984862	0.96[EUR][1000 genomes]
rs12336903	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12338164	0.94[EUR][1000 genomes]
rs12343945	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs13290142	0.94[EUR][1000 genomes]
rs28459874	0.94[EUR][1000 genomes]
rs28549286	0.94[EUR][1000 genomes]
rs28576751	0.94[EUR][1000 genomes]
rs28660049	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715400	0.94[EUR][1000 genomes]
rs66865656	0.93[EUR][1000 genomes]
rs7030197	0.92[EUR][1000 genomes]
rs7861102	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872251	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10984811	LPPR1	cis	parietal	SCAN
rs10984811	ANP32B	cis	cerebellum	SCAN
rs10984811	C9orf102	cis	parietal	SCAN
rs10984811	NANS	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100754600-100784200	Strong transcription	Dnd41	blood
2	chr9:100754600-100784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:100755600-100784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:100756400-100784400	Strong transcription	Fetal Thymus	thymus
5	chr9:100756600-100785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:100757000-100785200	Strong transcription	Placenta	Placenta
7	chr9:100757600-100784400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:100761800-100784400	Strong transcription	Thymus	Thymus
9	chr9:100762600-100785400	Strong transcription	Primary T cells from cord blood	blood
10	chr9:100764400-100784200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:100764400-100784200	Strong transcription	GM12878-XiMat	blood
12	chr9:100767000-100784600	Strong transcription	Fetal Stomach	stomach
13	chr9:100770200-100784200	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr9:100770600-100788400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:100771600-100784600	Strong transcription	Brain Hippocampus Middle	brain
16	chr9:100772200-100784200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr9:100772600-100784200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:100772600-100784400	Strong transcription	HSMMtube	muscle
19	chr9:100772800-100784400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr9:100773000-100784200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:100773000-100784400	Strong transcription	Lung	lung
22	chr9:100773000-100784600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:100773000-100784800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:100773200-100784200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:100773200-100785600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:100773400-100784200	Strong transcription	NHLF	lung
27	chr9:100773400-100784400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:100773400-100784600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:100773600-100784200	Strong transcription	Primary hematopoietic stem cells	blood
30	chr9:100776000-100785200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:100776400-100787400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:100778000-100784200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr9:100778800-100788400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr9:100779000-100784800	Weak transcription	NH-A	brain
35	chr9:100780000-100784200	Strong transcription	Gastric	stomach
36	chr9:100780000-100785200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr9:100780000-100788800	Weak transcription	Fetal Kidney	kidney
38	chr9:100781000-100785000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:100781200-100784800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:100781400-100788200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:100781600-100784200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:100781800-100784200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr9:100781800-100784600	Strong transcription	Fetal Muscle Leg	muscle
44	chr9:100781800-100785800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:100781800-100786000	Weak transcription	Fetal Brain Female	brain
46	chr9:100781800-100788800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:100781800-100791800	Weak transcription	Hela-S3	cervix
48	chr9:100781800-100796800	Weak transcription	Brain Anterior Caudate	brain
49	chr9:100781800-100796800	Weak transcription	Colon Smooth Muscle	Colon
50	chr9:100782000-100787800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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