Variant report

Variant	rs12653909
Chromosome Location	chr5:154188944-154188945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:154188887-154189083	K562	blood:	n/a	n/a
2	POLR2A	chr5:154188912-154189154	K562	blood:	n/a	n/a
3	POLR2A	chr5:154188814-154189117	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:154185736..154187394-chr5:154187487..154189195,2	K562	blood:
2	chr5:154187530..154189208-chr5:154202225..154204916,2	K562	blood:
3	chr5:154180336..154183354-chr5:154186581..154190474,5	MCF-7	breast:
4	chr5:154188897..154190397-chr5:154195933..154198821,2	K562	blood:

No data

Variant related genes	Relation type
LARP1	TF binding region
ENSG00000155506	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10434715	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs10463258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12652443	1.00[EUR][1000 genomes]
rs1467294	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17116362	1.00[EUR][1000 genomes]
rs17116407	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17116424	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17116430	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17116466	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4958768	1.00[AMR][1000 genomes];1.00[EUR][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	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154167000-154203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:154169200-154204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:154169200-154204200	Strong transcription	Dnd41	blood
4	chr5:154169400-154190400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr5:154169400-154191000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:154169400-154191200	Strong transcription	Primary T cells from cord blood	blood
7	chr5:154169400-154191200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:154169400-154191400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:154169400-154192600	Strong transcription	Fetal Thymus	thymus
10	chr5:154169400-154194800	Strong transcription	K562	blood
11	chr5:154169400-154198200	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr5:154169400-154198400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:154169400-154198800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:154169400-154199000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:154169400-154199400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr5:154169400-154200000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:154169400-154200800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr5:154169400-154201400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:154169400-154204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:154169400-154204200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:154169400-154204200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr5:154169400-154205800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:154169600-154189200	Strong transcription	Primary hematopoietic stem cells	blood
24	chr5:154169600-154191200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:154169600-154191600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:154169600-154192400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:154169600-154196400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:154169600-154199400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:154169600-154200000	Strong transcription	Fetal Muscle Leg	muscle
30	chr5:154169600-154202400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr5:154169600-154204200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr5:154169800-154189200	Strong transcription	Liver	Liver
33	chr5:154169800-154191000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:154169800-154191200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:154169800-154191400	Strong transcription	Brain Anterior Caudate	brain
36	chr5:154169800-154191600	Strong transcription	Primary B cells from cord blood	blood
37	chr5:154169800-154198200	Strong transcription	Fetal Brain Female	brain
38	chr5:154169800-154198600	Strong transcription	HMEC	breast
39	chr5:154170800-154201200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr5:154171000-154201000	Strong transcription	HSMM	muscle
41	chr5:154171200-154193200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:154171400-154189400	Strong transcription	GM12878-XiMat	blood
43	chr5:154172200-154191200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr5:154172800-154190800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:154174000-154212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:154174600-154190800	Strong transcription	A549	lung
47	chr5:154174800-154195600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:154174800-154204400	Strong transcription	Placenta	Placenta
49	chr5:154175000-154189200	Strong transcription	Hela-S3	cervix
50	chr5:154175000-154190400	Strong transcription	Adipose Nuclei	Adipose

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