Variant report

Variant	rs2877748
Chromosome Location	chr4:174102397-174102398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174089462..174093511-chr4:174101322..174108928,6	MCF-7	breast:
2	chr4:174088382..174092255-chr4:174100174..174103492,6	MCF-7	breast:
3	chr4:174102044..174104831-chr4:174106302..174107893,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109586	Chromatin interaction
ENSG00000245213	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10001613	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10011724	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10012395	0.81[ASN][1000 genomes]
rs10027708	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10031414	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10520252	0.81[ASN][1000 genomes]
rs1054496	0.95[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1054497	0.95[CEU][hapmap];0.92[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11737748	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes]
rs12503939	0.88[EUR][1000 genomes]
rs12639929	0.91[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs12644699	0.91[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs13111572	0.89[EUR][1000 genomes]
rs13125240	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs13138282	0.96[EUR][1000 genomes]
rs1574314	1.00[CEU][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17322893	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes]
rs1991727	0.91[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs2078475	0.97[EUR][1000 genomes]
rs2332654	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2332669	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs28477433	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28612521	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28701033	0.81[ASN][1000 genomes]
rs28709762	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733477	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4377567	0.91[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4419455	0.93[ASW][hapmap];0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4561909	0.95[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs4643788	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4695826	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6553679	0.89[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs6553680	0.81[ASN][1000 genomes]
rs6814857	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6826412	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835098	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6851632	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671278	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7672108	0.91[CEU][hapmap];0.90[GIH][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes]
rs9990666	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9997477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1793960	chr4:174090004-174102397	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1801469	chr4:174090004-174102397	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1823585	chr4:174090209-174107537	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174091600-174113600	Weak transcription	Esophagus	oesophagus
2	chr4:174091800-174104000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr4:174092600-174102400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:174092800-174103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:174092800-174103600	Weak transcription	Aorta	Aorta
6	chr4:174092800-174106000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:174092800-174109000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:174093600-174102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:174093600-174109800	Weak transcription	Gastric	stomach
10	chr4:174093800-174105000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:174094200-174102800	Weak transcription	Brain Anterior Caudate	brain
12	chr4:174095000-174109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:174095400-174102800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:174096200-174103200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:174096200-174111200	Weak transcription	Small Intestine	intestine
16	chr4:174096800-174103800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:174098000-174104200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr4:174098000-174106400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:174098600-174106200	Weak transcription	Fetal Thymus	thymus
20	chr4:174098800-174103800	Weak transcription	Thymus	Thymus
21	chr4:174098800-174104600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:174098800-174108400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:174099000-174106200	Weak transcription	Dnd41	blood
24	chr4:174099000-174109400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:174099200-174111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:174099600-174102800	Enhancers	A549	lung
27	chr4:174099800-174106000	Weak transcription	K562	blood
28	chr4:174100000-174102800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:174100000-174112200	Weak transcription	Brain Substantia Nigra	brain
30	chr4:174100200-174103800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:174100400-174103800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:174100400-174104200	Enhancers	Hela-S3	cervix
33	chr4:174100600-174103200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:174100800-174102400	Weak transcription	Fetal Intestine Large	intestine
35	chr4:174100800-174102800	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:174100800-174102800	Weak transcription	GM12878-XiMat	blood
37	chr4:174101000-174102400	Weak transcription	NHLF	lung
38	chr4:174101000-174102800	Weak transcription	NHEK	skin
39	chr4:174101000-174104600	Enhancers	HSMM	muscle
40	chr4:174101000-174106600	Weak transcription	Primary B cells from cord blood	blood
41	chr4:174101200-174102400	Enhancers	HUVEC	blood vessel
42	chr4:174101200-174106000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:174101400-174102400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:174101400-174102800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:174101400-174102800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:174101600-174102400	Weak transcription	NH-A	brain
47	chr4:174101600-174103800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:174101800-174103600	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr4:174101800-174104000	Enhancers	Primary hematopoietic stem cells	blood
50	chr4:174101800-174104600	Enhancers	Stomach Mucosa	stomach

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