Variant report

Variant	rs6894498
Chromosome Location	chr5:95140046-95140047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95140024..95141907-chr5:95144179..95145770,2	MCF-7	breast:
2	chr5:95133829..95136692-chr5:95138240..95141156,3	K562	blood:

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10515229	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12518592	0.81[EUR][1000 genomes]
rs12522843	1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs12522899	0.81[EUR][1000 genomes]
rs9784676	0.81[EUR][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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6894498	MCTP1	cis	cerebellum	SCAN
rs6894498	C5orf27	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95115400-95157000	Weak transcription	Aorta	Aorta
2	chr5:95117200-95143000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:95117200-95143200	Weak transcription	Primary T cells from cord blood	blood
4	chr5:95117200-95143400	Weak transcription	Thymus	Thymus
5	chr5:95117400-95144200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:95120800-95143400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:95121000-95156800	Weak transcription	Brain Germinal Matrix	brain
8	chr5:95124400-95143800	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:95124600-95143800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:95124600-95144000	Weak transcription	Brain Substantia Nigra	brain
11	chr5:95124600-95154400	Weak transcription	Brain Angular Gyrus	brain
12	chr5:95125000-95154400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:95125600-95140800	Weak transcription	GM12878-XiMat	blood
14	chr5:95126400-95143600	Weak transcription	Dnd41	blood
15	chr5:95127800-95149200	Weak transcription	Fetal Brain Female	brain
16	chr5:95128000-95143600	Weak transcription	Spleen	Spleen
17	chr5:95128000-95143800	Weak transcription	Lung	lung
18	chr5:95129800-95140200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:95129800-95143600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:95130000-95143600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:95130000-95145000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:95130000-95145000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:95130000-95157400	Weak transcription	Ovary	ovary
24	chr5:95130200-95140800	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:95130200-95143600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:95130200-95143600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:95130200-95143600	Weak transcription	Hela-S3	cervix
28	chr5:95130400-95146000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:95132800-95143600	Weak transcription	Fetal Stomach	stomach
30	chr5:95132800-95144200	Weak transcription	NHLF	lung
31	chr5:95133400-95142800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:95133400-95143400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:95133400-95144000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:95133600-95140600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:95133600-95144200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr5:95133600-95147800	Weak transcription	K562	blood
37	chr5:95134000-95143800	Weak transcription	HSMM	muscle
38	chr5:95134600-95140600	Enhancers	Fetal Intestine Large	intestine
39	chr5:95134800-95141000	Enhancers	Liver	Liver
40	chr5:95136400-95140800	Enhancers	Fetal Intestine Small	intestine
41	chr5:95137000-95140400	Enhancers	Duodenum Mucosa	Duodenum
42	chr5:95137000-95142400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:95137400-95140200	Enhancers	Placenta	Placenta
44	chr5:95137600-95141000	Weak transcription	Adipose Nuclei	Adipose
45	chr5:95137800-95140800	Enhancers	Fetal Kidney	kidney
46	chr5:95138000-95140800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr5:95138000-95141400	Weak transcription	Fetal Thymus	thymus
48	chr5:95138000-95143600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:95138400-95142800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:95139000-95143200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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