Variant report

Variant	rs168138
Chromosome Location	chr3:42668441-42668442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13064311	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13066173	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13066333	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2068278	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2271181	0.82[ASN][1000 genomes]
rs2271184	0.83[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271187	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2284305	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237064	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2940407	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3095258	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339656	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs339721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339724	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs339729	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs342523	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs342534	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs342535	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs342538	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs383937	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3888651	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs398743	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60994254	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612362	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs637852	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs638904	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs651180	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654761	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs663258	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs664813	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs665206	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs704982	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs807863	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs82755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311323	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9311324	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9813479	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9819563	0.93[ASN][1000 genomes]
rs9828279	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs168138	NKTR	cis	cerebellum	SCAN
rs168138	SNRK	cis	cerebellum	SCAN
rs168138	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs168138	NKTR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
3	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
7	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
9	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:42647000-42671400	Weak transcription	NHEK	skin
11	chr3:42647200-42668600	Weak transcription	Brain Germinal Matrix	brain
12	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:42647400-42672000	Weak transcription	NHLF	lung
14	chr3:42647600-42672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:42647600-42677600	Weak transcription	Gastric	stomach
16	chr3:42648800-42672600	Weak transcription	Fetal Brain Female	brain
17	chr3:42649800-42671200	Weak transcription	Fetal Brain Male	brain
18	chr3:42650400-42671400	Weak transcription	Thymus	Thymus
19	chr3:42650400-42671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:42650400-42672000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:42650600-42669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:42650600-42669400	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:42650600-42672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:42650600-42673000	Weak transcription	Esophagus	oesophagus
25	chr3:42650800-42672800	Weak transcription	Ovary	ovary
26	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:42651400-42671000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:42651800-42680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:42653400-42672000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:42653600-42672600	Weak transcription	Lung	lung
31	chr3:42653600-42672600	Weak transcription	Pancreas	Pancrea
32	chr3:42655000-42672400	Weak transcription	Right Ventricle	heart
33	chr3:42655000-42677800	Weak transcription	Small Intestine	intestine
34	chr3:42655200-42672000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:42655400-42672000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:42655400-42674400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:42656200-42688400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:42656600-42673000	Strong transcription	Hela-S3	cervix
39	chr3:42657400-42679600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:42657800-42669400	Weak transcription	Brain Substantia Nigra	brain
41	chr3:42657800-42672000	Weak transcription	Brain Angular Gyrus	brain
42	chr3:42658200-42669800	Weak transcription	A549	lung
43	chr3:42658200-42671400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:42658200-42673000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:42658200-42682200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:42658200-42693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:42658400-42691400	Strong transcription	Dnd41	blood
48	chr3:42658600-42669400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:42658600-42671000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:42658600-42671200	Weak transcription	Left Ventricle	heart

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