Variant report

Variant	rs55853397
Chromosome Location	chr6:54059113-54059114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10046453	1.00[AFR][1000 genomes]
rs12333151	0.98[AFR][1000 genomes]
rs28837994	0.86[AFR][1000 genomes]
rs56341219	0.81[AFR][1000 genomes]
rs57136553	0.83[AFR][1000 genomes]
rs58270498	0.81[AFR][1000 genomes]
rs6931929	0.98[AFR][1000 genomes]
rs73741456	0.93[AFR][1000 genomes]
rs73741459	1.00[AFR][1000 genomes]
rs73741462	1.00[AFR][1000 genomes]
rs73741464	1.00[AFR][1000 genomes]
rs73741469	0.88[AFR][1000 genomes]
rs73741470	0.88[AFR][1000 genomes]
rs73741473	0.88[AFR][1000 genomes]
rs73741475	0.86[AFR][1000 genomes]
rs73741481	0.86[AFR][1000 genomes]
rs7753902	0.86[AFR][1000 genomes]
rs9464029	0.98[AFR][1000 genomes]
rs9464031	0.98[AFR][1000 genomes]
rs9464036	0.86[AFR][1000 genomes]
rs9464040	0.81[AFR][1000 genomes]
rs9464041	0.81[AFR][1000 genomes]
rs9474756	0.98[AFR][1000 genomes]
rs9474757	1.00[AFR][1000 genomes]
rs9474758	1.00[AFR][1000 genomes]
rs9474759	1.00[AFR][1000 genomes]
rs9474763	0.86[AFR][1000 genomes]
rs9474764	0.86[AFR][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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv603110	chr6:53885918-54103794	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017633	chr6:53935336-54118476	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53998000-54099200	Weak transcription	Psoas Muscle	Psoas
2	chr6:54045800-54069200	Weak transcription	Fetal Heart	heart
3	chr6:54047200-54069600	Weak transcription	Right Ventricle	heart
4	chr6:54047400-54069600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:54055200-54069600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:54057400-54059600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:54057600-54059400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:54057600-54059400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:54057800-54059400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:54057800-54059400	Enhancers	NHLF	lung
11	chr6:54058000-54059200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr6:54058000-54059400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:54058000-54059400	Enhancers	HSMM	muscle
14	chr6:54058000-54059600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:54058000-54059800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr6:54058200-54059400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:54058200-54059400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:54058200-54059800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr6:54058400-54059200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:54058400-54059200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:54058400-54059200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:54058400-54059200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:54058400-54059200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:54058400-54059200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:54058400-54059200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:54058400-54059200	Enhancers	Fetal Muscle Leg	muscle
27	chr6:54058400-54059400	Enhancers	HSMMtube	muscle
28	chr6:54058400-54059400	Enhancers	NH-A	brain
29	chr6:54058400-54059600	Enhancers	HUVEC	blood vessel
30	chr6:54058600-54059200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:54058600-54059200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:54058600-54059200	Enhancers	NHEK	skin
33	chr6:54058800-54059400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:54058800-54101000	Weak transcription	Left Ventricle	heart
35	chr6:54059000-54059200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:54059000-54059200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links