Variant report

Variant	rs17106499
Chromosome Location	chr14:78331947-78331948
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78330457..78332124-chr14:78332590..78335145,2	K562	blood:

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

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

rs_ID	r²[population]
rs10139828	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10149767	0.83[CEU][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs10150446	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10150706	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11621593	0.82[JPT][hapmap]
rs11848126	1.00[ASN][1000 genomes]
rs11848358	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106478	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17106558	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1862125	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111829	0.82[JPT][hapmap]
rs28489182	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28613643	1.00[ASN][1000 genomes]
rs55708480	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55898434	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55956517	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55967811	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55976930	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56051443	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57859162	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61050485	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61053946	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493	0.82[JPT][hapmap]
rs7153025	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7160485	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72688844	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8009704	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015796	0.82[JPT][hapmap]
rs8018233	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8018945	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022914	0.88[ASN][1000 genomes]
rs9323652	0.88[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9323654	0.88[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9972189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[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	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17106499	NRXN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78297600-78336600	Weak transcription	Left Ventricle	heart
2	chr14:78297800-78353600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr14:78301400-78342200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr14:78306000-78356400	Weak transcription	Thymus	Thymus
5	chr14:78310000-78339400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:78310400-78345000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr14:78314200-78348400	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:78320800-78342200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr14:78321400-78342800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr14:78321800-78335400	Weak transcription	Psoas Muscle	Psoas
11	chr14:78321800-78348400	Weak transcription	Placenta	Placenta
12	chr14:78322000-78342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr14:78322000-78342600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr14:78322200-78353400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr14:78323400-78339600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr14:78324000-78353600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr14:78324200-78354800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr14:78324400-78339800	Weak transcription	Ovary	ovary
19	chr14:78325000-78332400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr14:78325000-78345000	Weak transcription	Brain Angular Gyrus	brain
21	chr14:78326400-78339800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr14:78326400-78342000	Weak transcription	Adipose Nuclei	Adipose
23	chr14:78326600-78352800	Weak transcription	Esophagus	oesophagus
24	chr14:78327000-78338000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr14:78327000-78339400	Weak transcription	Fetal Muscle Leg	muscle
26	chr14:78327000-78342000	Weak transcription	Lung	lung
27	chr14:78327200-78348600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr14:78327800-78400600	Weak transcription	Colonic Mucosa	Colon
29	chr14:78328000-78338200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr14:78328000-78353400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:78329000-78345000	Weak transcription	Brain Substantia Nigra	brain
32	chr14:78329000-78345800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr14:78329000-78347600	Weak transcription	Brain Anterior Caudate	brain
34	chr14:78329000-78348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr14:78329200-78345400	Weak transcription	Right Ventricle	heart
36	chr14:78329400-78336400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr14:78329400-78345200	Weak transcription	Brain Hippocampus Middle	brain
38	chr14:78330200-78332200	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr14:78330400-78334400	Strong transcription	Primary T cells from cord blood	blood
40	chr14:78330800-78334200	Weak transcription	Dnd41	blood
41	chr14:78331000-78333200	Weak transcription	Gastric	stomach
42	chr14:78331600-78332000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr14:78331600-78332000	Weak transcription	Spleen	Spleen
44	chr14:78331600-78332200	Strong transcription	Primary B cells from cord blood	blood
45	chr14:78331800-78332200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr14:78331800-78332200	Enhancers	Pancreas	Pancrea
47	chr14:78331800-78332200	Enhancers	K562	blood
48	chr14:78331800-78333200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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