Variant report

Variant	rs6670349
Chromosome Location	chr1:214517744-214517745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN14-1	chr1:214517515-214517753	ENSG00000228470.1

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1005709	0.83[ASN][1000 genomes]
rs10735513	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10779613	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10864092	0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11120290	0.81[ASN][1000 genomes]
rs11120292	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11120295	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11120309	0.81[CHB][hapmap]
rs1134647	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1135352	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12024395	0.82[ASN][1000 genomes]
rs12057464	0.82[ASN][1000 genomes]
rs12124666	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12137369	0.97[ASN][1000 genomes]
rs1472439	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1472443	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2270704	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2291829	0.86[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2291830	0.86[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2936014	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2936015	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2936016	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2936017	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2936018	0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes]
rs3002297	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3002298	0.83[JPT][hapmap];0.89[AMR][1000 genomes]
rs3002299	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3002300	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3002301	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3002303	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3002305	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3002306	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3002307	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3002308	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3002309	0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3002312	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3013442	1.00[ASW][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes]
rs3013446	1.00[ASW][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3013448	0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3013451	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3013452	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3013455	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4129186	0.81[CHB][hapmap]
rs4578186	1.00[ASW][hapmap];0.93[MKK][hapmap]
rs4655245	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4655335	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4655342	1.00[ASW][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];0.82[AMR][1000 genomes]
rs6540817	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs6540818	0.81[ASN][1000 genomes]
rs6540819	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6540820	0.82[ASN][1000 genomes]
rs6540821	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6540822	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6657368	1.00[ASW][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap]
rs6660940	0.84[ASN][1000 genomes]
rs6662275	0.82[ASN][1000 genomes]
rs6662864	0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6665343	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6673096	0.86[ASN][1000 genomes]
rs6687411	0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6691083	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6700976	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6701764	0.86[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs7413877	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7419021	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs7512745	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7530350	0.81[CHB][hapmap]
rs7550799	1.00[ASW][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes]
rs9429918	0.85[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6670349	RCOR3	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214484800-214522000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:214486200-214526000	Weak transcription	Psoas Muscle	Psoas
3	chr1:214488200-214520800	Weak transcription	Hela-S3	cervix
4	chr1:214490800-214518200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:214493000-214519800	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:214493000-214534600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:214493800-214519000	Weak transcription	Fetal Thymus	thymus
8	chr1:214501800-214517800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:214503200-214537800	Weak transcription	Gastric	stomach
10	chr1:214503400-214518400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:214504600-214533200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:214507000-214529800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:214508400-214517800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:214508400-214520000	Weak transcription	Thymus	Thymus
15	chr1:214508400-214524600	Weak transcription	Lung	lung
16	chr1:214508400-214524800	Weak transcription	Spleen	Spleen
17	chr1:214508400-214529600	Weak transcription	Pancreas	Pancrea
18	chr1:214508400-214535000	Weak transcription	Esophagus	oesophagus
19	chr1:214508800-214520400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:214508800-214528600	Weak transcription	Fetal Intestine Large	intestine
21	chr1:214509200-214523200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:214511200-214517800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:214511400-214524800	Weak transcription	Right Ventricle	heart
24	chr1:214511400-214529400	Weak transcription	Aorta	Aorta
25	chr1:214511400-214530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:214511400-214531200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:214511600-214522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:214511600-214528000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:214511800-214528000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:214512000-214518200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:214512000-214518200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:214512000-214520200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:214512000-214521600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:214512000-214537000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:214512400-214520800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:214512400-214524600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:214512600-214520400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:214512800-214518400	Weak transcription	HSMMtube	muscle
39	chr1:214513000-214519800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:214513200-214517800	Weak transcription	Dnd41	blood
41	chr1:214513600-214552200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:214513800-214518200	Weak transcription	Liver	Liver
43	chr1:214514000-214522600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:214514000-214523200	Strong transcription	Osteobl	bone
45	chr1:214514000-214537800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:214514200-214518000	Weak transcription	Primary T cells from cord blood	blood
47	chr1:214514400-214519000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:214514400-214523000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:214514600-214523200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:214514800-214519000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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