Variant report

Variant	rs28531897
Chromosome Location	chr14:69919113-69919114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10130642	0.86[ASN][1000 genomes]
rs10131446	0.87[AMR][1000 genomes]
rs10132626	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10142738	0.86[ASN][1000 genomes]
rs10148090	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11620664	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11622130	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11624753	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11624756	0.89[ASN][1000 genomes]
rs11626070	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11844803	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11847666	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185028	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12385913	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17106979	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17764155	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17836240	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1952255	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2015547	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061088	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2168241	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28616724	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6573886	0.85[AMR][1000 genomes]
rs7143230	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7152301	0.86[ASN][1000 genomes]
rs7155178	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7161463	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723815	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72723830	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72723840	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72723850	0.86[ASN][1000 genomes]
rs8016334	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016618	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9630395	0.83[AFR][1000 genomes];0.91[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	esv3396933	chr14:69906914-70001258	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28531897	SLC39A9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69868000-69923200	Weak transcription	Esophagus	oesophagus
2	chr14:69889200-69922400	Weak transcription	Brain Substantia Nigra	brain
3	chr14:69889200-69923400	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:69889400-69923200	Weak transcription	Pancreas	Pancrea
5	chr14:69890000-69922400	Weak transcription	Fetal Brain Male	brain
6	chr14:69890800-69922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:69891200-69922800	Weak transcription	Colonic Mucosa	Colon
8	chr14:69891200-69923000	Weak transcription	NHLF	lung
9	chr14:69892000-69920600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr14:69892200-69931400	Weak transcription	K562	blood
11	chr14:69893000-69919800	Weak transcription	Spleen	Spleen
12	chr14:69893000-69922800	Weak transcription	Aorta	Aorta
13	chr14:69893200-69926800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr14:69893400-69922200	Weak transcription	Left Ventricle	heart
15	chr14:69893400-69922400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr14:69893400-69922600	Weak transcription	Brain Germinal Matrix	brain
17	chr14:69893400-69922800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr14:69893400-69923000	Weak transcription	Lung	lung
19	chr14:69893600-69920200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr14:69893600-69920400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr14:69893600-69922000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr14:69893600-69922400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr14:69893600-69922400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr14:69893600-69922800	Weak transcription	Brain Hippocampus Middle	brain
25	chr14:69893600-69923200	Weak transcription	Gastric	stomach
26	chr14:69893600-69925000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr14:69894000-69922200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:69894000-69922800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr14:69894000-69924400	Weak transcription	Brain Angular Gyrus	brain
30	chr14:69894400-69919800	Weak transcription	Ovary	ovary
31	chr14:69894600-69919200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr14:69894600-69920600	Weak transcription	Adipose Nuclei	Adipose
33	chr14:69894600-69921800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr14:69894600-69922200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr14:69894600-69922800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr14:69895600-69919800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr14:69895600-69921400	Weak transcription	NH-A	brain
38	chr14:69896800-69922400	Weak transcription	Brain Anterior Caudate	brain
39	chr14:69897000-69922000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr14:69902400-69927000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr14:69903600-69922200	Weak transcription	Small Intestine	intestine
42	chr14:69903600-69937800	Weak transcription	Psoas Muscle	Psoas
43	chr14:69906600-69921400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr14:69906800-69921200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr14:69906800-69921400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr14:69906800-69922400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr14:69906800-69924400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:69906800-69924400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:69908200-69920400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr14:69908400-69922400	Weak transcription	Fetal Brain Female	brain

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