Variant report

Variant	rs860978
Chromosome Location	chr6:53949870-53949871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1325829	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4712054	1.00[YRI][hapmap]
rs4715439	1.00[YRI][hapmap]
rs612696	1.00[YRI][hapmap]
rs633124	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7762970	1.00[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv5307	chr6:53874118-53952230	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	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
7	nsv7901	chr6:53914491-53981080	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv823691	chr6:53918427-53978766	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv885885	chr6:53920024-54046264	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv34853	chr6:53924697-53977449	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv603120	chr6:53929484-53951857	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv603121	chr6:53929484-53951990	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53941400-53955000	Weak transcription	Right Ventricle	heart
2	chr6:53945000-53970800	Weak transcription	Right Atrium	heart
3	chr6:53948200-53950800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:53948200-53951000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:53948200-53951200	Enhancers	Fetal Heart	heart
6	chr6:53948600-53950000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:53948600-53950000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:53948600-53950000	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:53948600-53950000	Weak transcription	HSMMtube	muscle
10	chr6:53948600-53950400	Weak transcription	Brain Angular Gyrus	brain
11	chr6:53948800-53950000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:53949200-53950800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:53949200-53951400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:53949200-53951400	Enhancers	Adipose Nuclei	Adipose
15	chr6:53949200-53952400	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr6:53949400-53950000	Enhancers	Stomach Smooth Muscle	stomach
17	chr6:53949400-53951600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:53949600-53950200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr6:53949600-53950800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:53949600-53952600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:53949600-53953600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr6:53949800-53950200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:53949800-53950200	Flanking Active TSS	Psoas Muscle	Psoas
24	chr6:53949800-53950600	Enhancers	Left Ventricle	heart
25	chr6:53949800-53950600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:53949800-53950800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:53949800-53952400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:53949800-53953200	Enhancers	Fetal Muscle Leg	muscle

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