Variant report

Variant	rs6888220
Chromosome Location	chr5:79490620-79490621
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79488753..79490806-chr5:79550624..79553405,3	MCF-7	breast:
2	chr5:79485439..79488604-chr5:79489271..79493639,4	K562	blood:

Variant related genes	Relation type
ENSG00000164300	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10036141	1.00[ASN][1000 genomes]
rs10036779	1.00[ASN][1000 genomes]
rs10041410	1.00[ASN][1000 genomes]
rs10058560	1.00[ASN][1000 genomes]
rs10068511	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs12697906	1.00[ASN][1000 genomes]
rs13155466	1.00[CHD][hapmap]
rs13170471	1.00[ASN][1000 genomes]
rs13178966	1.00[ASN][1000 genomes]
rs13180605	1.00[ASN][1000 genomes]
rs13186313	1.00[CHD][hapmap]
rs13186656	1.00[ASN][1000 genomes]
rs13187742	1.00[ASN][1000 genomes]
rs13354808	0.88[CEU][hapmap]
rs13355153	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17200856	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17201124	1.00[ASN][1000 genomes]
rs2405138	1.00[ASN][1000 genomes]
rs2405141	1.00[CHD][hapmap]
rs28637244	1.00[ASN][1000 genomes]
rs35696683	1.00[ASN][1000 genomes]
rs4521455	1.00[ASN][1000 genomes]
rs56040222	1.00[ASN][1000 genomes]
rs6867389	1.00[ASN][1000 genomes]
rs6867803	1.00[ASN][1000 genomes]
rs6876065	1.00[ASN][1000 genomes]
rs71636208	1.00[ASN][1000 genomes]
rs72778006	1.00[ASN][1000 genomes]
rs72778028	1.00[ASN][1000 genomes]
rs7715187	1.00[CHD][hapmap]
rs9293805	0.87[CEU][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6888220	SCAMP1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79480200-79492400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr5:79481200-79490800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:79482200-79491000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr5:79483800-79496800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:79483800-79498200	Weak transcription	NHEK	skin
6	chr5:79485000-79490800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:79485200-79490800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:79485400-79491000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:79485800-79490800	Enhancers	Primary B cells from cord blood	blood
10	chr5:79486000-79491600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:79486400-79490800	Enhancers	Fetal Muscle Leg	muscle
12	chr5:79486400-79492000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:79486600-79490800	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr5:79486600-79490800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:79486600-79492000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:79487200-79491000	Enhancers	Placenta	Placenta
17	chr5:79487400-79490800	Enhancers	Adipose Nuclei	Adipose
18	chr5:79487400-79491000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:79487600-79490800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr5:79487600-79490800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr5:79487600-79490800	Enhancers	Fetal Brain Male	brain
22	chr5:79487600-79490800	Enhancers	Fetal Stomach	stomach
23	chr5:79487600-79490800	Enhancers	Left Ventricle	heart
24	chr5:79487600-79490800	Enhancers	Psoas Muscle	Psoas
25	chr5:79487600-79490800	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr5:79487600-79490800	Enhancers	Osteobl	bone
27	chr5:79487800-79490800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:79487800-79490800	Enhancers	Right Ventricle	heart
29	chr5:79487800-79490800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr5:79488000-79490800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr5:79488000-79490800	Enhancers	Right Atrium	heart
32	chr5:79488000-79491400	Enhancers	Liver	Liver
33	chr5:79488000-79492400	Enhancers	Brain Substantia Nigra	brain
34	chr5:79488200-79490800	Enhancers	Fetal Kidney	kidney
35	chr5:79488200-79491600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr5:79488200-79491800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:79488200-79491800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr5:79488200-79497200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:79488400-79490800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr5:79488400-79491800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr5:79488400-79492600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:79488600-79490800	Enhancers	Thymus	Thymus
43	chr5:79488600-79491600	Enhancers	Fetal Thymus	thymus
44	chr5:79488600-79493200	Enhancers	Brain Hippocampus Middle	brain
45	chr5:79488600-79497000	Weak transcription	Colonic Mucosa	Colon
46	chr5:79488800-79490800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr5:79488800-79490800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr5:79488800-79491800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:79488800-79492000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr5:79489000-79490800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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