Variant report

Variant	rs2780
Chromosome Location	chr1:214522085-214522086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN14-5	chr1:214522047-214523147	NONHSAT009458

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1007334	0.88[ASN][1000 genomes]
rs12086431	0.84[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs12131852	0.89[JPT][hapmap]
rs12725062	0.88[ASN][1000 genomes]
rs12726700	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12748030	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12748350	0.84[EUR][1000 genomes]
rs12750419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17786937	0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2133175	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.86[ASN][1000 genomes]
rs2291831	0.84[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34321892	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34442733	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35031581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35090781	0.80[EUR][1000 genomes]
rs35144729	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35345210	0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35723575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36116610	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3754135	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56356777	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6540826	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6668557	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6674564	1.00[AFR][1000 genomes]
rs66840032	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs66867382	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67229128	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs68118165	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7531372	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9786930	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2780	SYT14	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214486200-214526000	Weak transcription	Psoas Muscle	Psoas
2	chr1:214493000-214534600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:214503200-214537800	Weak transcription	Gastric	stomach
4	chr1:214504600-214533200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:214507000-214529800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:214508400-214524600	Weak transcription	Lung	lung
7	chr1:214508400-214524800	Weak transcription	Spleen	Spleen
8	chr1:214508400-214529600	Weak transcription	Pancreas	Pancrea
9	chr1:214508400-214535000	Weak transcription	Esophagus	oesophagus
10	chr1:214508800-214528600	Weak transcription	Fetal Intestine Large	intestine
11	chr1:214509200-214523200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:214511400-214524800	Weak transcription	Right Ventricle	heart
13	chr1:214511400-214529400	Weak transcription	Aorta	Aorta
14	chr1:214511400-214530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:214511400-214531200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:214511600-214522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:214511600-214528000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:214511800-214528000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:214512000-214537000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:214512400-214524600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:214513600-214552200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:214514000-214522600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:214514000-214523200	Strong transcription	Osteobl	bone
24	chr1:214514000-214537800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:214514400-214523000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:214514600-214523200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:214514800-214526400	Weak transcription	Fetal Stomach	stomach
28	chr1:214515400-214542600	Weak transcription	Brain Substantia Nigra	brain
29	chr1:214515800-214522400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:214516000-214522200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:214516000-214523200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:214516200-214522800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:214516400-214522600	Strong transcription	HSMM	muscle
34	chr1:214517200-214522200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:214517800-214523200	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:214518000-214522400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:214518000-214524600	Weak transcription	Left Ventricle	heart
38	chr1:214518400-214523800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:214518400-214537800	Weak transcription	Fetal Brain Male	brain
40	chr1:214518600-214523200	Weak transcription	A549	lung
41	chr1:214518600-214524800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:214518600-214524800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:214518600-214529000	Weak transcription	Ovary	ovary
44	chr1:214518800-214522400	Weak transcription	Fetal Heart	heart
45	chr1:214518800-214524600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:214518800-214528800	Weak transcription	Fetal Kidney	kidney
47	chr1:214519000-214523000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:214519000-214523000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:214519000-214523400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:214519000-214524000	Weak transcription	Primary T cells from cord blood	blood

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