Variant report

Variant	rs7872881
Chromosome Location	chr9:26838839-26838840
allele	G/T
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]
rs10511793	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs10812492	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs10812500	1.00[JPT][hapmap]
rs10967594	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs10967625	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs12338262	0.85[CEU][hapmap];0.96[GIH][hapmap]
rs12342005	1.00[JPT][hapmap]
rs12344894	0.86[AFR][1000 genomes]
rs12352441	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs16910888	1.00[JPT][hapmap]
rs16910895	1.00[JPT][hapmap]
rs17693955	0.92[CEU][hapmap];0.93[GIH][hapmap]
rs59274950	0.91[EUR][1000 genomes]
rs62544443	0.91[EUR][1000 genomes]
rs62544450	0.91[EUR][1000 genomes]
rs62544451	0.88[EUR][1000 genomes]
rs62544452	0.91[EUR][1000 genomes]
rs6475948	1.00[JPT][hapmap]
rs7023230	0.91[EUR][1000 genomes]
rs7035755	1.00[CEU][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs7039400	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs7040516	1.00[JPT][hapmap]
rs7045881	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs7851339	0.90[EUR][1000 genomes]
rs7851423	0.82[EUR][1000 genomes]
rs7851582	0.89[EUR][1000 genomes]
rs7860542	0.85[CEU][hapmap]
rs7871097	1.00[JPT][hapmap]
rs7871286	1.00[JPT][hapmap]

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	nsv1026827	chr9:26693515-26904699	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3373096	chr9:26825001-26848031	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7872881	C9orf82	cis	parietal	SCAN
rs7872881	IFT74	Cis_1M	lymphoblastoid	RTeQTL
rs7872881	IFT74	cis	lymphoblastoid	seeQTL
rs7872881	C9orf82	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26822200-26889400	Weak transcription	Psoas Muscle	Psoas
2	chr9:26822600-26846200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:26829000-26839400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:26829000-26839600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:26829000-26840200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:26829000-26840400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:26829200-26842200	Weak transcription	Left Ventricle	heart
8	chr9:26830200-26865400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:26832200-26866800	Weak transcription	Gastric	stomach
10	chr9:26832200-26878400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:26833000-26839600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:26833800-26842200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:26834000-26839600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:26834000-26840800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:26834000-26882400	Weak transcription	HUVEC	blood vessel
16	chr9:26834200-26839600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:26834200-26840800	Weak transcription	Placenta	Placenta
18	chr9:26834200-26842000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:26834200-26842400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:26834200-26842400	Weak transcription	HSMM	muscle
21	chr9:26834200-26849800	Weak transcription	Fetal Thymus	thymus
22	chr9:26834200-26852800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:26834200-26852800	Weak transcription	HSMMtube	muscle
24	chr9:26834200-26853400	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:26834200-26854800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:26834200-26855000	Weak transcription	Ovary	ovary
27	chr9:26834200-26858800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:26834200-26859000	Weak transcription	Fetal Kidney	kidney
29	chr9:26834200-26870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:26834200-26878400	Weak transcription	Brain Angular Gyrus	brain
31	chr9:26834200-26878600	Weak transcription	Spleen	Spleen
32	chr9:26834200-26880200	Weak transcription	Lung	lung
33	chr9:26834200-26880200	Weak transcription	NHEK	skin
34	chr9:26834200-26882200	Weak transcription	HMEC	breast
35	chr9:26834200-26888200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr9:26834200-26891200	Weak transcription	NHDF-Ad	bronchial
37	chr9:26834400-26840400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:26834400-26840600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:26834400-26854800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr9:26835800-26842200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr9:26836200-26839400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:26836200-26839600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr9:26836200-26840400	Weak transcription	Adipose Nuclei	Adipose
44	chr9:26836200-26854200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr9:26836400-26839600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:26836400-26839800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:26836400-26842200	Weak transcription	Primary T cells from cord blood	blood
48	chr9:26836400-26842200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:26836400-26842600	Weak transcription	Dnd41	blood
50	chr9:26836400-26849000	Weak transcription	Primary B cells from cord blood	blood

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