Variant report

Variant	rs6426549
Chromosome Location	chr1:227015552-227015553
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226898679..226899853-chr1:227014945..227016440,5	MCF-7	breast:
2	chr1:226735526..226736066-chr1:227015394..227016390,2	K562	blood:
3	chr1:226827872..226829435-chr1:227013407..227016393,2	MCF-7	breast:
4	chr1:226889929..226892747-chr1:227013300..227016016,3	MCF-7	breast:
5	chr1:226821864..226822630-chr1:227015469..227016387,6	MCF-7	breast:
6	chr1:226821563..226822762-chr1:227015422..227016864,5	K562	blood:
7	chr1:226834406..226836488-chr1:227013877..227016506,3	K562	blood:
8	chr1:227006518..227010110-chr1:227013321..227015905,5	K562	blood:
9	chr1:226898884..226899407-chr1:227015534..227016163,2	MCF-7	breast:
10	chr1:226821201..226822498-chr1:227015438..227016431,9	MCF-7	breast:
11	chr1:226813787..226814594-chr1:227015029..227016132,3	MCF-7	breast:
12	chr1:226814100..226814798-chr1:227015543..227016441,4	K562	blood:
13	chr1:226898531..226899526-chr1:227015550..227016285,3	K562	blood:
14	chr1:226831819..226832498-chr1:227015490..227016147,2	MCF-7	breast:
15	chr1:227014350..227016521-chr17:57915564..57918181,2	MCF-7	breast:

No data

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11580744	0.81[EUR][1000 genomes]
rs12733650	0.81[EUR][1000 genomes]
rs16846644	0.95[CEU][hapmap]
rs1800672	0.95[CEU][hapmap]
rs1800673	0.95[CEU][hapmap]
rs1800681	0.95[CEU][hapmap]
rs3213436	0.95[CEU][hapmap]
rs35396772	0.81[EUR][1000 genomes]
rs6426550	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426554	0.95[CEU][hapmap]
rs6676067	0.95[CEU][hapmap]
rs6689397	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs732479	0.95[CEU][hapmap]
rs7512804	0.81[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6426549	PSEN2	cis	cerebellum	SCAN
rs6426549	PSEN2	cis	parietal	SCAN
rs6426549	ARF1	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227009800-227015600	Weak transcription	Osteobl	bone
2	chr1:227010000-227015600	Weak transcription	Left Ventricle	heart
3	chr1:227011400-227016000	Enhancers	Brain Hippocampus Middle	brain
4	chr1:227011600-227015600	Enhancers	Brain Anterior Caudate	brain
5	chr1:227013200-227016400	Enhancers	Fetal Muscle Trunk	muscle
6	chr1:227013400-227016200	Enhancers	GM12878-XiMat	blood
7	chr1:227013600-227015600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:227013600-227016200	Enhancers	Placenta	Placenta
9	chr1:227014200-227016200	Enhancers	Fetal Muscle Leg	muscle
10	chr1:227014400-227015800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:227014600-227015600	Enhancers	Adipose Nuclei	Adipose
12	chr1:227014600-227015600	Enhancers	Brain Angular Gyrus	brain
13	chr1:227014600-227015600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr1:227014600-227015800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:227014600-227015800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:227014600-227015800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:227014600-227015800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:227014600-227015800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:227014600-227015800	Enhancers	Colonic Mucosa	Colon
20	chr1:227014600-227015800	Enhancers	Colon Smooth Muscle	Colon
21	chr1:227014600-227015800	Enhancers	Fetal Heart	heart
22	chr1:227014600-227015800	Enhancers	Lung	lung
23	chr1:227014600-227016000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr1:227014600-227016200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:227014800-227015600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr1:227014800-227015600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:227014800-227015600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:227014800-227015600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:227014800-227015600	Enhancers	NHDF-Ad	bronchial
30	chr1:227014800-227015800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr1:227014800-227015800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:227014800-227016200	Enhancers	Primary T cells from cord blood	blood
33	chr1:227014800-227016200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:227014800-227016200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:227014800-227016200	Enhancers	Fetal Stomach	stomach
36	chr1:227015000-227015600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:227015000-227015600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:227015000-227015600	Enhancers	Thymus	Thymus
39	chr1:227015000-227015800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr1:227015000-227015800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr1:227015000-227016000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:227015000-227016000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:227015000-227016000	Enhancers	Stomach Mucosa	stomach
44	chr1:227015000-227016000	Enhancers	NHLF	lung
45	chr1:227015000-227016200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:227015000-227016200	Enhancers	Fetal Thymus	thymus
47	chr1:227015000-227016400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr1:227015200-227015600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr1:227015200-227015600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:227015200-227015600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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