Variant report

Variant	rs9857442
Chromosome Location	chr3:23946235-23946236
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10865790	0.85[CHB][hapmap]
rs1133926	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1136155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706297	0.87[ASN][1000 genomes]
rs11710647	0.87[ASN][1000 genomes]
rs11710679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11711073	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11711380	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713246	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12497944	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13314607	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13318927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325754	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1397880	0.87[ASN][1000 genomes]
rs1567581	0.90[ASN][1000 genomes]
rs17014081	0.82[ASN][1000 genomes]
rs17787211	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2089848	0.82[JPT][hapmap]
rs2361013	0.87[ASN][1000 genomes]
rs28522849	0.87[ASN][1000 genomes]
rs28623591	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34476593	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35711415	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35886023	0.87[ASN][1000 genomes]
rs4131864	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs60699428	0.82[ASN][1000 genomes]
rs61294694	0.87[ASN][1000 genomes]
rs61645368	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62253361	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62253380	0.90[ASN][1000 genomes]
rs62253382	0.90[ASN][1000 genomes]
rs62253383	0.82[ASN][1000 genomes]
rs62253387	0.84[ASN][1000 genomes]
rs6550809	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6765292	1.00[CHB][hapmap]
rs6768429	1.00[CHB][hapmap]
rs6778970	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6787216	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800407	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72627066	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73825116	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73825124	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73825170	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73825178	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73825181	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7629325	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7637968	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938078	0.87[ASN][1000 genomes]
rs9815334	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834166	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9836860	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838694	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9850255	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856727	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9863605	0.84[ASN][1000 genomes]
rs9863674	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9875213	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9876561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9857442	NR1D2	cis	Temporal Cortex	GTEx
rs9857442	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL
rs9857442	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23916000-23950200	Weak transcription	Aorta	Aorta
2	chr3:23916200-23948800	Weak transcription	Colonic Mucosa	Colon
3	chr3:23922400-23956600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:23923000-23956600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:23923400-23955200	Weak transcription	Thymus	Thymus
6	chr3:23923400-23957000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:23923600-23956800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:23924200-23957800	Weak transcription	Esophagus	oesophagus
9	chr3:23924200-23957800	Weak transcription	Lung	lung
10	chr3:23928000-23957200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:23928800-23956000	Weak transcription	Small Intestine	intestine
12	chr3:23928800-23957400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:23929000-23956600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:23930800-23954800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:23930800-23956800	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:23932000-23955400	Weak transcription	NHEK	skin
17	chr3:23934200-23956600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:23934400-23956400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:23934600-23947600	Strong transcription	Fetal Stomach	stomach
20	chr3:23935000-23957400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:23935800-23954400	Weak transcription	NH-A	brain
22	chr3:23935800-23954600	Weak transcription	HUVEC	blood vessel
23	chr3:23936400-23951600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:23936400-23951800	Weak transcription	Spleen	Spleen
25	chr3:23936400-23956400	Weak transcription	Psoas Muscle	Psoas
26	chr3:23936800-23957200	Weak transcription	Brain Substantia Nigra	brain
27	chr3:23937000-23956600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:23938400-23946600	Strong transcription	Liver	Liver
29	chr3:23938400-23947000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:23939800-23956600	Weak transcription	Fetal Brain Male	brain
31	chr3:23940400-23956600	Weak transcription	Pancreas	Pancrea
32	chr3:23940600-23948400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:23940600-23950800	Weak transcription	Brain Angular Gyrus	brain
34	chr3:23940600-23956600	Weak transcription	Brain Germinal Matrix	brain
35	chr3:23940600-23956800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:23940800-23947000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:23940800-23955400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:23940800-23956200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:23940800-23956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:23940800-23956400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:23940800-23956600	Weak transcription	Left Ventricle	heart
42	chr3:23940800-23956600	Weak transcription	NHLF	lung
43	chr3:23940800-23957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:23940800-23957200	Weak transcription	Right Ventricle	heart
45	chr3:23941000-23947200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:23941000-23951200	Weak transcription	Fetal Lung	lung
47	chr3:23941000-23956000	Weak transcription	HMEC	breast
48	chr3:23941000-23956600	Weak transcription	Primary B cells from cord blood	blood
49	chr3:23941200-23951800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:23941200-23952400	Weak transcription	Fetal Brain Female	brain

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