Variant report

Variant	rs6535556
Chromosome Location	chr4:148665206-148665207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148651355..148654142-chr4:148663991..148665938,2	MCF-7	breast:
2	chr4:148655157..148657016-chr4:148664536..148666375,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071205	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10027921	0.90[JPT][hapmap]
rs10776520	1.00[CEU][hapmap]
rs11099669	1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs11725260	0.88[EUR][1000 genomes]
rs11729081	0.90[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs12502667	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12640660	0.90[JPT][hapmap];1.00[MEX][hapmap]
rs12645249	0.90[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs12648074	0.80[AMR][1000 genomes]
rs13119467	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs13134018	0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs13144139	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1604785	0.90[JPT][hapmap]
rs1969102	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2055551	0.86[AMR][1000 genomes]
rs2118036	0.86[MEX][hapmap]
rs2134706	0.90[JPT][hapmap]
rs28505821	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4490438	0.84[EUR][1000 genomes]
rs4835093	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4835448	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56946313	0.85[EUR][1000 genomes]
rs6535558	0.86[AMR][1000 genomes]
rs6535559	0.86[AMR][1000 genomes]
rs6535561	0.88[JPT][hapmap];0.80[AMR][1000 genomes]
rs6822971	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs6827786	0.85[AMR][1000 genomes]
rs6828600	1.00[CEU][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs6836509	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6839987	0.86[AMR][1000 genomes]
rs6845560	0.86[AMR][1000 genomes]
rs7661297	1.00[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs7669809	0.88[EUR][1000 genomes]
rs7673234	0.86[AMR][1000 genomes]
rs7673606	0.90[JPT][hapmap];0.86[AMR][1000 genomes]
rs905606	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs9332471	0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs964170	0.90[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][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	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880242	chr4:148659137-148727355	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148655600-148681600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:148655800-148665600	Weak transcription	Lung	lung
3	chr4:148656600-148676800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:148656800-148675200	Weak transcription	Fetal Stomach	stomach
5	chr4:148657000-148668600	Weak transcription	Gastric	stomach
6	chr4:148657400-148668600	Weak transcription	Fetal Intestine Small	intestine
7	chr4:148658200-148665400	Weak transcription	Aorta	Aorta
8	chr4:148658200-148675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:148658800-148665400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:148659200-148668000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:148660800-148668200	Weak transcription	Fetal Intestine Large	intestine
12	chr4:148663000-148675200	Weak transcription	Fetal Lung	lung
13	chr4:148663200-148665400	Weak transcription	Esophagus	oesophagus
14	chr4:148663200-148665400	Weak transcription	Left Ventricle	heart
15	chr4:148663200-148670800	Weak transcription	A549	lung
16	chr4:148663200-148674400	Weak transcription	NHLF	lung
17	chr4:148663200-148675200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:148663200-148675200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:148663200-148675200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:148663400-148665400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:148663400-148665400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:148663400-148665400	Weak transcription	Right Atrium	heart
23	chr4:148663400-148665400	Weak transcription	Right Ventricle	heart
24	chr4:148663400-148665400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:148663400-148665600	Weak transcription	Ovary	ovary
26	chr4:148663400-148665600	Weak transcription	Psoas Muscle	Psoas
27	chr4:148663400-148667800	Weak transcription	GM12878-XiMat	blood
28	chr4:148663400-148668000	Weak transcription	Fetal Heart	heart
29	chr4:148663400-148668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:148663400-148668200	Weak transcription	HSMMtube	muscle
31	chr4:148663400-148668600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:148663400-148668600	Weak transcription	Adipose Nuclei	Adipose
33	chr4:148663400-148668600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:148663400-148668600	Weak transcription	NHEK	skin
35	chr4:148663400-148669000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:148663400-148670800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:148663400-148670800	Weak transcription	NH-A	brain
38	chr4:148663400-148674600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:148663400-148674600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:148663400-148674800	Weak transcription	HUVEC	blood vessel
41	chr4:148663400-148675000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:148663400-148675000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:148663400-148675000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:148663400-148675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:148663400-148675000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:148663600-148666000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:148663600-148666200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:148663600-148674200	Weak transcription	Osteobl	bone
49	chr4:148663600-148674800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:148663600-148675200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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