Variant report

Variant	rs7859253
Chromosome Location	chr9:108483741-108483742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10115634	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10118720	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10119254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10512339	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739209	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10739210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739212	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759127	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10759129	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816293	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271247	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271248	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3105993	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3126471	0.81[JPT][hapmap]
rs3793640	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6477461	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7019359	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7026251	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7039618	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7039893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7859125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862873	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9299110	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv615116	chr9:108468129-108546438	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7859253	LPPR1	cis	parietal	SCAN
rs7859253	OR13C2	cis	parietal	SCAN
rs7859253	TMEM38B	cis	lymphoblastoid	seeQTL
rs7859253	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108457800-108492200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108458000-108497800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr9:108458200-108491400	Weak transcription	HSMMtube	muscle
4	chr9:108458200-108491600	Weak transcription	Brain Anterior Caudate	brain
5	chr9:108458200-108495400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:108458200-108497000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:108459200-108489400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:108463200-108496800	Weak transcription	HepG2	liver
9	chr9:108463400-108487600	Weak transcription	Primary B cells from cord blood	blood
10	chr9:108465000-108496600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr9:108469000-108485000	Weak transcription	Small Intestine	intestine
12	chr9:108470600-108497000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr9:108470800-108487200	Weak transcription	Liver	Liver
14	chr9:108470800-108496000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:108471000-108495400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:108473200-108487200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:108473200-108490800	Weak transcription	Fetal Lung	lung
18	chr9:108473200-108496400	Weak transcription	Primary T cells from cord blood	blood
19	chr9:108473200-108497200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr9:108473200-108499800	Weak transcription	Gastric	stomach
21	chr9:108473400-108492200	Weak transcription	GM12878-XiMat	blood
22	chr9:108475400-108492600	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:108475800-108488000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:108476200-108485800	Weak transcription	Right Ventricle	heart
25	chr9:108476200-108497800	Weak transcription	Psoas Muscle	Psoas
26	chr9:108476400-108491400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:108476400-108498200	Weak transcription	Left Ventricle	heart
28	chr9:108476600-108483800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:108476600-108488000	Weak transcription	Fetal Stomach	stomach
30	chr9:108476600-108493800	Weak transcription	Ovary	ovary
31	chr9:108476800-108483800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:108476800-108485600	Weak transcription	Fetal Intestine Large	intestine
33	chr9:108476800-108487800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr9:108476800-108491400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:108477000-108489600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:108477200-108483800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:108477200-108485400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:108477200-108485800	Weak transcription	Fetal Intestine Small	intestine
39	chr9:108477200-108487600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:108477200-108493400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:108477200-108495400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr9:108478800-108487600	Weak transcription	K562	blood
43	chr9:108479000-108487200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:108479000-108490000	Weak transcription	Fetal Heart	heart
45	chr9:108481600-108497600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:108482000-108488800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr9:108482000-108489600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr9:108482200-108496600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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