Variant report

Variant	rs3754540
Chromosome Location	chr2:63813458-63813459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63812159..63813845-chr2:63813874..63816684,2	MCF-7	breast:
2	chr2:63802150..63804372-chr2:63812471..63815243,3	K562	blood:

Variant related genes	Relation type
ENSG00000014641	Chromatin interaction
ENSG00000143951	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10164844	0.82[JPT][hapmap]
rs10171190	0.81[CHB][hapmap]
rs10200146	0.81[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10209490	0.81[CHB][hapmap]
rs1022351	0.81[CHB][hapmap]
rs1022353	0.81[CHB][hapmap]
rs11125979	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676682	0.91[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11694892	0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap]
rs12104978	0.84[ASN][1000 genomes]
rs12995715	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13409031	0.81[CHB][hapmap]
rs13422170	0.81[CHB][hapmap]
rs169035	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1869700	0.91[ASN][1000 genomes]
rs1878505	0.82[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap]
rs2028886	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2034270	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs2138791	0.81[CHB][hapmap]
rs2178678	0.81[CHB][hapmap]
rs2421891	0.84[CHB][hapmap]
rs2421892	0.81[CHB][hapmap]
rs2421954	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2422008	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs2592389	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs262496	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs262497	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs262498	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs262499	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs262500	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35516797	0.85[EUR][1000 genomes]
rs4671061	0.81[CHB][hapmap]
rs4671511	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6731136	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6731877	0.82[ASN][1000 genomes]
rs6735907	0.86[CHB][hapmap]
rs6737621	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6756850	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7598973	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs8179835	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][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	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1792289	chr2:63812148-63900292	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63780200-63814800	Weak transcription	Psoas Muscle	Psoas
2	chr2:63801000-63814400	Weak transcription	Primary B cells from cord blood	blood
3	chr2:63806000-63813600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:63806200-63813600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:63806200-63814000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:63808600-63813800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:63808600-63814200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:63808800-63813600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:63808800-63814800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:63809000-63813600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:63809000-63813800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:63809000-63813800	Weak transcription	Brain Substantia Nigra	brain
13	chr2:63809000-63814200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:63809000-63814200	Weak transcription	Osteobl	bone
15	chr2:63809200-63813600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:63809200-63813600	Weak transcription	Liver	Liver
17	chr2:63809200-63813600	Weak transcription	NHEK	skin
18	chr2:63809200-63813800	Weak transcription	Brain Anterior Caudate	brain
19	chr2:63809200-63813800	Weak transcription	Right Atrium	heart
20	chr2:63809200-63814000	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:63809200-63814000	Weak transcription	NHDF-Ad	bronchial
22	chr2:63809200-63814200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:63809200-63814200	Weak transcription	Adipose Nuclei	Adipose
24	chr2:63809200-63814200	Weak transcription	Right Ventricle	heart
25	chr2:63809200-63814600	Weak transcription	Stomach Mucosa	stomach
26	chr2:63809200-63814800	Weak transcription	Left Ventricle	heart
27	chr2:63809400-63814200	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:63809800-63813800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:63809800-63814400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:63809800-63814800	Weak transcription	Thymus	Thymus
31	chr2:63810400-63814200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:63811200-63813600	Weak transcription	K562	blood
33	chr2:63811800-63814600	Weak transcription	Fetal Stomach	stomach
34	chr2:63812400-63813600	Enhancers	Dnd41	blood
35	chr2:63813000-63817800	Active TSS	H1 Cell Line	embryonic stem cell
36	chr2:63813200-63813600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:63813400-63813600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr2:63813400-63813600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:63813400-63813800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:63813400-63813800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:63813400-63814000	Flanking Active TSS	GM12878-XiMat	blood
42	chr2:63813400-63814200	Enhancers	HepG2	liver
43	chr2:63813400-63814800	Enhancers	Fetal Heart	heart
44	chr2:63813400-63817400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:63813400-63817400	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr2:63813400-63817600	Active TSS	HUES48 Cell Line	embryonic stem cell

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