Variant report

Variant	rs2160838
Chromosome Location	chr14:77804405-77804406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77802533..77804704-chr14:77806659..77809069,2	MCF-7	breast:
2	chr14:77802289..77805136-chr14:77808966..77810650,2	K562	blood:
3	chr14:77803636..77806540-chr14:77808690..77810650,2	K562	blood:
4	chr14:77801139..77804066-chr14:77804282..77807434,3	K562	blood:
5	chr14:77799211..77800820-chr14:77802677..77804757,2	MCF-7	breast:
6	chr14:77796973..77800849-chr14:77803398..77806096,3	MCF-7	breast:
7	chr14:77790302..77791930-chr14:77801928..77804820,2	K562	blood:

Variant related genes	Relation type
ENSG00000100577	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10132619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046428	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11845842	0.93[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11847091	1.00[CHD][hapmap]
rs11850308	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11850771	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12881799	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12886056	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12887558	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12893462	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12894718	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468951	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105724	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1861887	0.90[ASN][1000 genomes]
rs1861888	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs2111700	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2160839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160840	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2270419	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs2363640	0.85[ASN][1000 genomes]
rs2364155	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3209079	0.86[CHB][hapmap]
rs3759731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815625	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs383064	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs4141640	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs4903566	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs56162150	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67845205	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7155184	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73311369	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73311375	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8005730	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8014716	0.85[ASN][1000 genomes]
rs9671248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv902107	chr14:77790416-77871777	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2160838	TMED8	cis	Skin Sun Exposed Lower leg	GTEx
rs2160838	PAPLN	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77788600-77806000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr14:77788600-77806200	Weak transcription	Thymus	Thymus
3	chr14:77788800-77804600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:77788800-77805200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr14:77788800-77806400	Weak transcription	Colonic Mucosa	Colon
6	chr14:77789000-77805200	Weak transcription	Osteobl	bone
7	chr14:77789000-77805400	Weak transcription	Primary T cells from cord blood	blood
8	chr14:77789000-77805400	Weak transcription	A549	lung
9	chr14:77789000-77805600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:77789000-77805600	Weak transcription	Left Ventricle	heart
11	chr14:77789000-77805800	Weak transcription	Fetal Thymus	thymus
12	chr14:77789000-77806000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr14:77789000-77806000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr14:77789000-77806000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:77789000-77806000	Weak transcription	Colon Smooth Muscle	Colon
16	chr14:77789000-77806200	Weak transcription	Brain Hippocampus Middle	brain
17	chr14:77789000-77806200	Weak transcription	Lung	lung
18	chr14:77789000-77806400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr14:77789000-77807600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:77789200-77805200	Weak transcription	Fetal Intestine Large	intestine
21	chr14:77789200-77805400	Weak transcription	GM12878-XiMat	blood
22	chr14:77789200-77805600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr14:77789200-77805600	Weak transcription	Fetal Brain Female	brain
24	chr14:77789200-77805600	Weak transcription	Pancreas	Pancrea
25	chr14:77789200-77805800	Weak transcription	Fetal Muscle Leg	muscle
26	chr14:77789200-77805800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr14:77789200-77805800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr14:77789200-77806200	Weak transcription	Fetal Lung	lung
29	chr14:77789200-77806400	Weak transcription	Esophagus	oesophagus
30	chr14:77789200-77806800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr14:77789200-77807000	Weak transcription	Brain Angular Gyrus	brain
32	chr14:77789200-77818200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr14:77789400-77805800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr14:77789400-77806200	Weak transcription	Brain Germinal Matrix	brain
35	chr14:77789600-77806200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr14:77791600-77807400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr14:77792400-77806400	Weak transcription	Placenta	Placenta
38	chr14:77793200-77824600	Weak transcription	Psoas Muscle	Psoas
39	chr14:77794400-77807800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr14:77796000-77804600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr14:77796400-77806400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr14:77796800-77807600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr14:77797000-77806200	Weak transcription	Gastric	stomach
44	chr14:77797000-77807800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr14:77798200-77806200	Weak transcription	Spleen	Spleen
46	chr14:77798400-77806200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr14:77798600-77806000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr14:77799200-77806000	Weak transcription	Dnd41	blood
49	chr14:77799400-77808800	Weak transcription	K562	blood
50	chr14:77799800-77805400	Weak transcription	Brain Cingulate Gyrus	brain

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