Variant report

Variant	rs4557282
Chromosome Location	chr4:77999178-77999179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77997759..78000070-chr4:78123881..78125820,2	MCF-7	breast:
2	chr4:77993925..77999822-chr4:78072652..78081114,32	MCF-7	breast:
3	chr4:77994543..78000148-chr4:78076403..78082799,9	K562	blood:
4	chr4:77995405..77999334-chr4:78000731..78006327,9	MCF-7	breast:
5	chr4:77994107..77999899-chr4:78076204..78082875,32	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEPT11-2	chr4:77997130-77999849	NONHSAT097041

Variant related genes	Relation type
ENSG00000138764	Chromatin interaction
ENSG00000214062	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10002443	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs10006033	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs10031961	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10470896	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs10856952	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs11559161	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs12186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12644714	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1472399	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs16996592	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs17002332	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs17002334	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17002336	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs17002339	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs17002346	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17002420	1.00[MEX][hapmap]
rs17002482	1.00[MEX][hapmap]
rs2009261	1.00[MEX][hapmap]
rs2016811	1.00[CEU][hapmap]
rs2279711	0.80[CHB][hapmap]
rs2645668	1.00[GIH][hapmap]
rs28715145	0.98[ASN][1000 genomes]
rs41375744	1.00[MEX][hapmap]
rs41495248	1.00[MEX][hapmap]
rs4252773	1.00[GIH][hapmap]
rs4252775	1.00[MEX][hapmap]
rs4252813	0.91[ASN][1000 genomes]
rs4252858	0.98[ASN][1000 genomes]
rs4252887	0.94[ASN][1000 genomes]
rs4252896	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs4252897	0.94[ASN][1000 genomes]
rs4252913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4252930	0.93[ASN][1000 genomes]
rs4252934	1.00[MEX][hapmap]
rs4859740	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6817626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818356	1.00[MEX][hapmap]
rs6824360	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6837546	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840204	1.00[MEX][hapmap]
rs7667891	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];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	nsv879499	chr4:77990904-78003416	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77997800-78000400	Weak transcription	Spleen	Spleen
2	chr4:77998000-77999400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:77998000-77999400	Enhancers	Small Intestine	intestine
4	chr4:77998000-77999400	Flanking Active TSS	Dnd41	blood
5	chr4:77998000-77999600	Weak transcription	Left Ventricle	heart
6	chr4:77998000-77999800	Enhancers	Primary B cells from peripheral blood	blood
7	chr4:77998000-78000400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:77998000-78000400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:77998000-78000600	Weak transcription	Lung	lung
10	chr4:77998200-77999200	Enhancers	Fetal Stomach	stomach
11	chr4:77998200-77999400	Enhancers	Fetal Brain Male	brain
12	chr4:77998200-77999800	Enhancers	Fetal Muscle Leg	muscle
13	chr4:77998200-78004200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:77998400-77999400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:77998400-77999400	Enhancers	Fetal Kidney	kidney
16	chr4:77998400-77999400	Enhancers	Fetal Lung	lung
17	chr4:77998400-77999400	Enhancers	HMEC	breast
18	chr4:77998400-77999400	Enhancers	HSMMtube	muscle
19	chr4:77998400-78000000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:77998400-78000200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr4:77998400-78000200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:77998400-78000800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:77998400-78004200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:77998400-78004400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:77998400-78013800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:77998400-78016800	Weak transcription	Aorta	Aorta
27	chr4:77998600-77999200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:77998600-77999200	Enhancers	Brain Germinal Matrix	brain
29	chr4:77998600-77999200	Enhancers	Brain Hippocampus Middle	brain
30	chr4:77998600-77999200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr4:77998600-77999200	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr4:77998600-77999400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr4:77998600-77999400	Enhancers	Fetal Brain Female	brain
34	chr4:77998600-77999400	Enhancers	GM12878-XiMat	blood
35	chr4:77998600-77999600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:77998600-77999800	Enhancers	Fetal Thymus	thymus
37	chr4:77998600-77999800	Enhancers	NHEK	skin
38	chr4:77998600-78000000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr4:77998600-78000000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:77998600-78000600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr4:77998600-78001200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr4:77998600-78002600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:77998600-78003600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:77998600-78004400	Weak transcription	Placenta	Placenta
45	chr4:77998600-78004600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:77998800-77999200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:77998800-77999200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:77998800-77999200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr4:77998800-77999200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:77998800-77999400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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