Variant report

Variant	rs6535561
Chromosome Location	chr4:148694658-148694659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:148693468..148695247-chr4:148729923..148731609,2	K562	blood:
2	chr4:148649361..148653898-chr4:148687606..148694872,6	MCF-7	breast:
3	chr4:148691338..148693292-chr4:148693665..148695844,2	MCF-7	breast:
4	chr4:148692638..148695831-chr4:148697652..148700222,4	MCF-7	breast:
5	chr4:148692827..148694690-chr4:148699168..148701568,2	K562	blood:

Variant related genes	Relation type
ENSG00000240014	Chromatin interaction
ENSG00000071205	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10027921	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11099669	0.82[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1119887	1.00[JPT][hapmap]
rs11729081	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502667	0.80[AMR][1000 genomes]
rs12640660	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12645249	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650280	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13116955	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13134018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13136202	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13136624	0.82[AFR][1000 genomes]
rs13136858	0.83[AFR][1000 genomes]
rs1604785	0.85[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs17023844	1.00[JPT][hapmap]
rs2055551	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2118036	0.92[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2134706	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164527	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6535556	0.88[JPT][hapmap];0.80[AMR][1000 genomes]
rs6535558	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6535559	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6535560	0.98[AFR][1000 genomes]
rs6822971	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6829479	0.83[AMR][1000 genomes]
rs6836509	0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs6837391	0.83[AMR][1000 genomes]
rs6839987	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6840039	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6845560	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7673234	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7673606	0.82[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs964170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148679200-148696400	Weak transcription	Lung	lung
2	chr4:148687200-148696400	Weak transcription	Right Ventricle	heart
3	chr4:148689400-148698000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:148689600-148700200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr4:148689800-148699400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:148689800-148700400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:148690400-148695000	Enhancers	Fetal Heart	heart
8	chr4:148691200-148695600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:148691200-148696800	Enhancers	Psoas Muscle	Psoas
10	chr4:148691400-148697800	Enhancers	Fetal Intestine Small	intestine
11	chr4:148692200-148696800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:148692400-148697600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:148692800-148695200	Enhancers	Stomach Mucosa	stomach
14	chr4:148692800-148695600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:148692800-148695600	Enhancers	NHDF-Ad	bronchial
16	chr4:148693000-148695000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr4:148693000-148695600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:148693000-148695800	Enhancers	Fetal Intestine Large	intestine
19	chr4:148693200-148694800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:148693200-148695000	Enhancers	GM12878-XiMat	blood
21	chr4:148693200-148695000	Flanking Active TSS	NHEK	skin
22	chr4:148693200-148695200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:148693200-148695200	Enhancers	A549	lung
24	chr4:148693200-148695200	Flanking Active TSS	NH-A	brain
25	chr4:148693200-148695600	Enhancers	Adipose Nuclei	Adipose
26	chr4:148693200-148695600	Enhancers	Fetal Stomach	stomach
27	chr4:148693200-148696000	Enhancers	HMEC	breast
28	chr4:148693200-148696400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:148693200-148697000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:148693200-148700600	Enhancers	Colon Smooth Muscle	Colon
31	chr4:148693400-148694800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr4:148693400-148694800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:148693400-148695000	Flanking Active TSS	HUVEC	blood vessel
34	chr4:148693400-148695200	Enhancers	Fetal Lung	lung
35	chr4:148693400-148696000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:148693400-148697000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr4:148693400-148697800	Weak transcription	Pancreas	Pancrea
38	chr4:148693600-148695000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:148693600-148695000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr4:148693600-148695000	Weak transcription	Aorta	Aorta
41	chr4:148693600-148695400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:148693600-148695800	Enhancers	NHLF	lung
43	chr4:148693600-148696000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:148693600-148696000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:148693600-148696400	Weak transcription	Right Atrium	heart
46	chr4:148693600-148697200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr4:148693600-148697400	Weak transcription	Esophagus	oesophagus
48	chr4:148693800-148695000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:148693800-148695000	Weak transcription	Left Ventricle	heart
50	chr4:148693800-148695000	Weak transcription	Ovary	ovary

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