Variant report

Variant	rs3754534
Chromosome Location	chr2:152685880-152685881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCLAF1	chr2:152685066-152685887	K562	blood:	n/a	n/a
2	MAFK	chr2:152684971-152685880	K562	blood:	n/a	chr2:152685674-152685689 chr2:152685677-152685691 chr2:152685669-152685689
3	POLR2A	chr2:152684033-152685886	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr2:152684586-152685956	A549	lung:	n/a	chr2:152685001-152685011

No.	Distal block	Cell Line	Cell type
1	chr2:152684763..152686807-chr2:153031833..153033553,2	MCF-7	breast:
2	chr2:152657917..152660487-chr2:152685208..152686908,2	K562	blood:
3	chr2:152685053..152687897-chr2:152732170..152734670,2	K562	blood:

Variant related genes	Relation type
ARL5A	TF binding region
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12624108	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16830417	1.00[EUR][1000 genomes]
rs3754533	1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3768654	1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4077123	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs59269531	1.00[EUR][1000 genomes]
rs72621646	1.00[AMR][1000 genomes]
rs72621647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72621648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72621649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152685200-152686000	Flanking Active TSS	HepG2	liver
2	chr2:152685400-152686400	Weak transcription	Spleen	Spleen
3	chr2:152685400-152688200	Enhancers	Fetal Intestine Large	intestine
4	chr2:152685400-152697200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:152685600-152686000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr2:152685600-152686600	Weak transcription	Small Intestine	intestine
7	chr2:152685600-152687200	Weak transcription	Aorta	Aorta
8	chr2:152685600-152687600	Enhancers	Fetal Intestine Small	intestine
9	chr2:152685600-152688600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:152685600-152694600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:152685600-152695200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:152685600-152697600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:152685600-152699400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:152685600-152709600	Weak transcription	Fetal Brain Female	brain
15	chr2:152685800-152686600	Enhancers	Adipose Nuclei	Adipose
16	chr2:152685800-152686600	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:152685800-152686600	Enhancers	K562	blood
18	chr2:152685800-152689800	Weak transcription	GM12878-XiMat	blood
19	chr2:152685800-152690000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:152685800-152690400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr2:152685800-152690400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:152685800-152690400	Weak transcription	Primary B cells from cord blood	blood
23	chr2:152685800-152690400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:152685800-152690400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:152685800-152690400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:152685800-152692000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:152685800-152695200	Weak transcription	Brain Anterior Caudate	brain
28	chr2:152685800-152695600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:152685800-152697400	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:152685800-152699200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:152685800-152699400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:152685800-152702200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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