Variant report

Variant	rs11625045
Chromosome Location	chr14:65549089-65549090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHURC1-FNTB-1	chr14:65548752-65549100	ENSG00000259118.1

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10151162	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs11158572	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11158573	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11158574	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1124751	0.84[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs1124752	0.84[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs11626156	0.90[ASN][1000 genomes]
rs11626496	0.86[ASN][1000 genomes]
rs11627382	0.84[MEX][hapmap]
rs11627859	0.86[ASN][1000 genomes]
rs12147959	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1256417	0.86[EUR][1000 genomes]
rs1270074	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs1271582	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12880781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12884836	0.85[ASN][1000 genomes]
rs12887607	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12888794	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12893404	0.85[ASN][1000 genomes]
rs17825846	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs1953228	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1953232	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1957948	0.84[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1998688	0.84[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs2093989	0.91[EUR][1000 genomes]
rs2763888	0.81[EUR][1000 genomes]
rs2781373	0.84[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs2781374	0.83[EUR][1000 genomes]
rs2898863	0.89[ASN][1000 genomes]
rs34062462	0.89[ASN][1000 genomes]
rs35002541	0.89[ASN][1000 genomes]
rs35176994	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35769504	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3783720	0.91[ASW][hapmap];0.80[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap]
rs45604339	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4899160	0.90[ASW][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap]
rs4899161	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4902357	0.82[EUR][1000 genomes]
rs4902358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902359	0.83[EUR][1000 genomes]
rs4902360	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4902361	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4902364	0.86[ASN][1000 genomes]
rs4902365	0.86[ASN][1000 genomes]
rs4902367	0.89[ASN][1000 genomes]
rs55658675	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7143495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7144259	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7150646	0.83[EUR][1000 genomes]
rs7154852	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7156617	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs7159443	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs7160037	0.91[ASW][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap]
rs7161394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs762810	1.00[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8004805	0.83[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8009396	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8009714	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8010213	0.86[EUR][1000 genomes]
rs8015330	0.84[ASN][1000 genomes]
rs8181937	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181938	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs868814	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.90[ASN][1000 genomes]
rs884683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942626	0.84[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs942627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942628	0.84[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][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	nsv832816	chr14:65473244-65644645	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11625045	RAB15	cis	lymphoblastoid	seeQTL
rs11625045	WDR89	cis	cerebellum	SCAN
rs11625045	SIX4	cis	cerebellum	SCAN
rs11625045	MAX	cis	cerebellum	SCAN
rs11625045	MAX	cis	parietal	SCAN
rs11625045	RAB15	cis	cerebellum	SCAN
rs11625045	GPX2	cis	cerebellum	SCAN
rs11625045	CHURC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65527800-65553600	Strong transcription	Dnd41	blood
2	chr14:65528800-65555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:65530000-65553000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:65534000-65553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr14:65534800-65553400	Strong transcription	Thymus	Thymus
6	chr14:65536000-65553600	Strong transcription	Fetal Thymus	thymus
7	chr14:65538800-65553600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr14:65538800-65562000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr14:65539000-65551000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr14:65539000-65562400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:65539200-65550800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr14:65539200-65551400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:65539400-65551000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr14:65539400-65552400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:65539600-65563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr14:65539800-65553200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:65541000-65551600	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr14:65541600-65551000	Strong transcription	NH-A	brain
19	chr14:65541600-65552400	Strong transcription	Hela-S3	cervix
20	chr14:65541800-65549800	Strong transcription	HepG2	liver
21	chr14:65542400-65550400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr14:65542800-65550800	Strong transcription	Fetal Lung	lung
23	chr14:65543000-65550800	Strong transcription	HSMMtube	muscle
24	chr14:65543400-65549200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr14:65543800-65551000	Genic enhancers	Fetal Intestine Large	intestine
26	chr14:65544000-65552400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr14:65544400-65553600	Weak transcription	Fetal Brain Male	brain
28	chr14:65544600-65551400	Genic enhancers	Fetal Intestine Small	intestine
29	chr14:65544600-65553600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:65544800-65550600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr14:65544800-65551400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr14:65544800-65552400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr14:65544800-65552400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr14:65545000-65549200	Genic enhancers	Primary monocytes fromperipheralblood	blood
35	chr14:65545400-65563000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:65545600-65549600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr14:65545600-65549600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr14:65545600-65549800	Genic enhancers	Primary T cells from cord blood	blood
39	chr14:65545600-65551000	Enhancers	Right Atrium	heart
40	chr14:65545600-65551000	Enhancers	Right Ventricle	heart
41	chr14:65545600-65552400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr14:65545600-65552600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
43	chr14:65545800-65549200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr14:65545800-65549200	Enhancers	Stomach Mucosa	stomach
45	chr14:65545800-65550000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr14:65545800-65551000	Strong transcription	NHLF	lung
47	chr14:65545800-65551800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr14:65545800-65552000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr14:65546000-65550800	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr14:65546000-65550800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--

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