Variant report

Variant	rs7028281
Chromosome Location	chr9:98712182-98712183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10121403	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10481647	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739632	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10760675	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10760692	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12004422	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12553442	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1410783	0.88[ASN][1000 genomes]
rs1928253	0.86[ASN][1000 genomes]
rs3930253	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4743458	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs583716	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs585223	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs591579	0.88[ASN][1000 genomes]
rs601916	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs615866	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs617884	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs626264	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs631273	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs636456	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs640281	0.81[AMR][1000 genomes]
rs643815	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6479036	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs676453	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs680468	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs680754	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs683829	0.88[ASN][1000 genomes]
rs689627	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs689749	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689820	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689871	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs689979	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs690222	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs690304	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs690335	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs690420	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs690455	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs690484	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7024710	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7868559	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7874897	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs913408	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1035723	chr9:98701628-98734356	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7028281	LINC00476	cis	lung	GTEx
rs7028281	LINC00476	cis	Stomach	GTEx
rs7028281	LINC00476	cis	Thyroid	GTEx
rs7028281	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs7028281	LINC00476	cis	Artery Aorta	GTEx
rs7028281	LINC00476	cis	Nerve Tibial	GTEx
rs7028281	LINC00476	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
3	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
4	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
6	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr9:98687800-98718400	Weak transcription	Stomach Mucosa	stomach
8	chr9:98687800-98726000	Weak transcription	Gastric	stomach
9	chr9:98695600-98718200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:98695800-98742400	Weak transcription	NHLF	lung
11	chr9:98697800-98713200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:98699600-98717600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:98699800-98718600	Weak transcription	NHEK	skin
14	chr9:98702400-98718600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:98702400-98718600	Weak transcription	Small Intestine	intestine
16	chr9:98702600-98718600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:98702600-98718600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:98702600-98718600	Weak transcription	Aorta	Aorta
19	chr9:98702600-98718600	Weak transcription	Pancreas	Pancrea
20	chr9:98704000-98714200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:98705000-98718600	Weak transcription	K562	blood
22	chr9:98705000-98718800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:98705200-98716200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:98705400-98734200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
26	chr9:98706800-98734000	Weak transcription	Hela-S3	cervix
27	chr9:98707800-98712200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:98708000-98712200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr9:98708200-98712200	ZNF genes & repeats	Fetal Brain Female	brain
30	chr9:98708200-98712200	ZNF genes & repeats	Fetal Lung	lung
31	chr9:98708400-98712800	ZNF genes & repeats	Fetal Intestine Large	intestine
32	chr9:98708800-98712400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
33	chr9:98709000-98712200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:98709000-98713800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:98709000-98714000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:98709200-98718200	Weak transcription	NHDF-Ad	bronchial
37	chr9:98709400-98716200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr9:98709600-98718600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:98709800-98716200	Weak transcription	Adipose Nuclei	Adipose
40	chr9:98709800-98716400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr9:98709800-98717000	Weak transcription	Thymus	Thymus
42	chr9:98709800-98718600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:98709800-98718600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr9:98709800-98718600	Weak transcription	Left Ventricle	heart
45	chr9:98709800-98718800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:98709800-98718800	Weak transcription	Right Ventricle	heart
47	chr9:98709800-98727800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:98710000-98718200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr9:98710000-98718400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr9:98710000-98718400	Weak transcription	NH-A	brain

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