Variant report

Variant	rs11720964
Chromosome Location	chr3:49336232-49336233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11130184	0.82[CEU][hapmap]
rs11552724	1.00[JPT][hapmap]
rs11709788	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11920251	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12493284	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12497569	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12629759	0.82[CEU][hapmap];0.88[MKK][hapmap]
rs12637576	0.82[CEU][hapmap]
rs12715435	0.86[ASN][1000 genomes]
rs13077723	0.90[ASN][1000 genomes]
rs13078949	1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1865741	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2117938	0.82[CEU][hapmap];0.88[MKK][hapmap]
rs2230929	0.86[ASN][1000 genomes]
rs34142492	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34567776	0.81[ASN][1000 genomes]
rs34915642	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs35174559	0.88[MKK][hapmap]
rs35869135	0.81[ASN][1000 genomes]
rs3774799	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4554002	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4955431	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4955432	0.82[CEU][hapmap]
rs67882627	0.83[ASN][1000 genomes]
rs6795772	0.83[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7374375	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7640903	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7652746	0.82[CEU][hapmap];0.84[MKK][hapmap]
rs9818758	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[JPT][hapmap]
rs9863142	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9864406	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9873994	0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[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	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs11720964	NCKIPSD	cis	cerebellum	SCAN
rs11720964	WDR6	cis	Nerve Tibial	GTEx
rs11720964	WDR6	cis	Artery Tibial	GTEx
rs11720964	WDR6	cis	lymphoblastoid	seeQTL
rs11720964	AMT	cis	cerebellum	SCAN
rs11720964	DALRD3	cis	parietal	SCAN
rs11720964	C3orf62	cis	cerebellum	SCAN
rs11720964	CCDC71	cis	cerebellum	SCAN
rs11720964	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11720964	AMT	cis	Thyroid	GTEx
rs11720964	WDR6	cis	Whole Blood	GTEx
rs11720964	AMT	cis	parietal	SCAN
rs11720964	P4HTM	cis	cerebellum	SCAN
rs11720964	DALRD3	cis	cerebellum	SCAN
rs11720964	P4HTM	cis	parietal	SCAN
rs11720964	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs11720964	WDR6	cis	cerebellum	SCAN
rs11720964	WDR6	cis	parietal	SCAN
rs11720964	WDR6	cis	Muscle Skeletal	GTEx
rs11720964	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49313200-49349400	Strong transcription	Dnd41	blood
3	chr3:49313600-49349200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:49314800-49355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:49315200-49349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:49315200-49349600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49315200-49352600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
11	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
12	chr3:49315800-49349200	Strong transcription	Fetal Brain Female	brain
13	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:49316600-49340200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:49317200-49349400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
17	chr3:49317400-49349200	Strong transcription	Fetal Intestine Large	intestine
18	chr3:49317400-49349600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:49319400-49349600	Strong transcription	Liver	Liver
23	chr3:49319600-49344000	Strong transcription	Osteobl	bone
24	chr3:49319600-49349400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:49319800-49349200	Strong transcription	Brain Germinal Matrix	brain
27	chr3:49319800-49349400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:49320000-49337600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:49320000-49340600	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr3:49320000-49349000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:49320000-49349600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:49320200-49375000	Strong transcription	Thymus	Thymus
33	chr3:49320400-49338400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:49320600-49340600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:49320600-49351400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:49320800-49340200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:49320800-49342200	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr3:49320800-49344200	Strong transcription	Primary B cells from cord blood	blood
39	chr3:49320800-49349200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:49320800-49349400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:49320800-49368000	Strong transcription	Primary T cells from cord blood	blood
42	chr3:49321000-49348400	Strong transcription	NH-A	brain
43	chr3:49321800-49373600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:49326800-49373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:49326800-49375000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:49329400-49340600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:49329400-49340600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:49329400-49343600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:49329400-49344000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:49329600-49340600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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