Variant report

Variant	rs2354580
Chromosome Location	chr16:48637178-48637179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:48636374..48639117-chr16:48642848..48644889,3	MCF-7	breast:
2	chr16:48632564..48634928-chr16:48635026..48637928,2	MCF-7	breast:
3	chr16:48631319..48633375-chr16:48635515..48637561,2	K562	blood:
4	chr16:48416397..48419006-chr16:48635531..48637181,2	K562	blood:

Variant related genes	Relation type
ENSG00000102921	Chromatin interaction
ENSG00000260033	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12918232	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2047601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3785138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3826176	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4028695	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs4315324	0.89[AMR][1000 genomes]
rs6500392	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6500393	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8046716	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8057605	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9930255	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2354580	LCE1B	trans	parietal	SCAN
rs2354580	NKD1	cis	cerebellum	SCAN
rs2354580	PAPD5	cis	cerebellum	SCAN
rs2354580	NOD2	cis	cerebellum	SCAN
rs2354580	N4BP1	cis	multi-tissue	Pritchard
rs2354580	C16orf78	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48618200-48640400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr16:48626400-48640400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:48628400-48639800	Weak transcription	A549	lung
4	chr16:48628600-48637400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr16:48629800-48639800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr16:48629800-48640000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr16:48629800-48641800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr16:48630000-48638600	Enhancers	Primary T cells from cord blood	blood
9	chr16:48630000-48641200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr16:48630000-48641600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr16:48630200-48639200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr16:48630400-48638800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr16:48630400-48639800	Weak transcription	Fetal Thymus	thymus
14	chr16:48630400-48642600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr16:48630600-48641000	Weak transcription	HSMMtube	muscle
16	chr16:48630800-48637400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:48631000-48637200	Weak transcription	Pancreas	Pancrea
18	chr16:48631000-48637400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr16:48631800-48637200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr16:48631800-48637200	Weak transcription	NHEK	skin
21	chr16:48631800-48637800	Weak transcription	K562	blood
22	chr16:48631800-48639400	Weak transcription	Thymus	Thymus
23	chr16:48631800-48639800	Weak transcription	Fetal Stomach	stomach
24	chr16:48632000-48637200	Weak transcription	Brain Angular Gyrus	brain
25	chr16:48632000-48637200	Weak transcription	Gastric	stomach
26	chr16:48632000-48637400	Weak transcription	Fetal Muscle Leg	muscle
27	chr16:48632000-48637800	Weak transcription	NHDF-Ad	bronchial
28	chr16:48632000-48639600	Weak transcription	Placenta	Placenta
29	chr16:48632000-48640200	Weak transcription	HSMM	muscle
30	chr16:48632200-48637200	Weak transcription	Brain Anterior Caudate	brain
31	chr16:48632200-48637600	Weak transcription	Aorta	Aorta
32	chr16:48632200-48639200	Weak transcription	HMEC	breast
33	chr16:48632200-48639400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr16:48632200-48639400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:48632200-48639800	Weak transcription	Dnd41	blood
36	chr16:48632200-48641000	Weak transcription	Osteobl	bone
37	chr16:48632400-48637200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr16:48632400-48637600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr16:48632400-48639600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:48632400-48640400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr16:48632600-48637400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr16:48632800-48637200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr16:48632800-48640800	Weak transcription	Hela-S3	cervix
44	chr16:48633000-48638400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr16:48633000-48639800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr16:48633200-48639400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr16:48633400-48637200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr16:48633400-48637200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr16:48633400-48637400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr16:48633400-48637400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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