Variant report

Variant	rs874610
Chromosome Location	chr9:100782695-100782696
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100779905..100783686-chr9:100794453..100797990,3	K562	blood:
2	chr9:100781552..100783540-chr9:100791010..100793557,2	MCF-7	breast:
3	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: 2 )

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

rs_ID	r²[population]
rs1059273	0.80[CEU][hapmap]
rs12001675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12554172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16912622	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs3739672	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742716	0.80[CEU][hapmap]
rs4743150	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743151	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743157	0.80[CEU][hapmap];0.87[MEX][hapmap]
rs4743158	0.80[CEU][hapmap]
rs6478522	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478539	0.80[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap]
rs6478556	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs7019033	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7020081	0.80[CEU][hapmap]
rs7041878	0.88[ASN][1000 genomes]
rs7850685	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852752	0.89[CHB][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap]
rs7855432	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869762	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs957955	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs874610	LPPR1	cis	parietal	SCAN
rs874610	HIATL1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100752000-100784000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100754600-100784200	Strong transcription	Dnd41	blood
3	chr9:100754600-100784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:100755200-100783800	Strong transcription	NHEK	skin
5	chr9:100755400-100783000	Weak transcription	Stomach Mucosa	stomach
6	chr9:100755600-100784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:100756400-100783600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:100756400-100783800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr9:100756400-100784400	Strong transcription	Fetal Thymus	thymus
10	chr9:100756600-100785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:100756800-100783000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:100756800-100783400	Strong transcription	HMEC	breast
13	chr9:100757000-100785200	Strong transcription	Placenta	Placenta
14	chr9:100757200-100783600	Strong transcription	Liver	Liver
15	chr9:100757400-100784000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr9:100757600-100784400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:100760800-100783600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:100761800-100784400	Strong transcription	Thymus	Thymus
19	chr9:100762600-100785400	Strong transcription	Primary T cells from cord blood	blood
20	chr9:100764400-100784200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:100764400-100784200	Strong transcription	GM12878-XiMat	blood
22	chr9:100765600-100783000	Weak transcription	Right Atrium	heart
23	chr9:100765800-100782800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr9:100765800-100784000	Strong transcription	Adipose Nuclei	Adipose
25	chr9:100766400-100783400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:100767000-100784600	Strong transcription	Fetal Stomach	stomach
27	chr9:100767200-100783200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:100768200-100784000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:100770200-100784200	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr9:100770600-100788400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:100771600-100784600	Strong transcription	Brain Hippocampus Middle	brain
32	chr9:100772200-100784200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr9:100772400-100783600	Strong transcription	A549	lung
34	chr9:100772600-100784200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:100772600-100784400	Strong transcription	HSMMtube	muscle
36	chr9:100772800-100784400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr9:100773000-100782800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:100773000-100783200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:100773000-100783400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:100773000-100784000	Strong transcription	Spleen	Spleen
41	chr9:100773000-100784200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:100773000-100784400	Strong transcription	Lung	lung
43	chr9:100773000-100784600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:100773000-100784800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:100773200-100784200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr9:100773200-100785600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr9:100773400-100784000	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr9:100773400-100784200	Strong transcription	NHLF	lung
49	chr9:100773400-100784400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:100773400-100784600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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