Variant report

Variant	rs28893517
Chromosome Location	chr6:29565373-29565374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29564159..29568485-chr6:29574849..29577852,4	K562	blood:
2	chr6:29565212..29568130-chr6:29573289..29574813,2	K562	blood:
3	chr6:29556939..29558806-chr6:29563836..29566834,2	K562	blood:
4	chr6:29564780..29575712-chr6:29592511..29597522,14	K562	blood:
5	chr6:29560060..29561694-chr6:29565009..29566876,2	K562	blood:
6	chr6:29564159..29568485-chr6:29574849..29577852,3	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12524535	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12525400	0.86[EUR][1000 genomes]
rs12528017	0.81[EUR][1000 genomes]
rs12530421	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17178028	0.81[EUR][1000 genomes]
rs2267635	0.81[EUR][1000 genomes]
rs28749531	0.95[ASN][1000 genomes]
rs28893512	0.86[EUR][1000 genomes]
rs28893514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28893515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28893516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28986296	0.81[EUR][1000 genomes]
rs28986297	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28986298	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28986300	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28986301	0.83[EUR][1000 genomes]
rs28986303	0.95[EUR][1000 genomes]
rs28986306	0.95[EUR][1000 genomes]
rs28986307	0.93[EUR][1000 genomes]
rs28986308	0.81[EUR][1000 genomes]
rs29242	0.81[EUR][1000 genomes]
rs29255	0.86[EUR][1000 genomes]
rs3025645	0.93[EUR][1000 genomes]
rs3025646	0.95[EUR][1000 genomes]
rs3025649	0.81[EUR][1000 genomes]
rs362521	0.83[EUR][1000 genomes]
rs41286283	0.86[EUR][1000 genomes]
rs41286287	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41291762	0.81[EUR][1000 genomes]
rs41291766	0.81[EUR][1000 genomes]
rs41291770	0.90[AFR][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv5239	chr6:29527407-29566446	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29546200-29569400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:29559400-29568400	Weak transcription	HMEC	breast
3	chr6:29561200-29567800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:29561400-29567200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:29561400-29567600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:29561600-29567600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:29561600-29567600	Weak transcription	Fetal Stomach	stomach
8	chr6:29561600-29569000	Weak transcription	Spleen	Spleen
9	chr6:29561600-29569400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:29561600-29569600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:29561600-29569800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:29561600-29570000	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:29561600-29570000	Weak transcription	Lung	lung
14	chr6:29561600-29570000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:29561600-29570200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:29561600-29570600	Weak transcription	Right Ventricle	heart
17	chr6:29561600-29571600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:29561800-29566600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:29561800-29569400	Weak transcription	Fetal Lung	lung
20	chr6:29561800-29570200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:29561800-29571600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:29561800-29573200	Weak transcription	HSMMtube	muscle
23	chr6:29562000-29566200	Weak transcription	Ovary	ovary
24	chr6:29562000-29566800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:29562000-29567800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:29562000-29568400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:29562000-29569200	Weak transcription	Brain Anterior Caudate	brain
28	chr6:29562000-29569400	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:29562000-29569800	Weak transcription	K562	blood
30	chr6:29562000-29570600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:29562000-29571800	Weak transcription	Left Ventricle	heart
32	chr6:29562000-29572600	Weak transcription	Fetal Heart	heart
33	chr6:29563000-29566000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:29563000-29566800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:29563000-29567400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:29563000-29569000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:29563000-29569400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr6:29563200-29566800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:29563400-29569000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:29563800-29566800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:29564000-29566600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr6:29564000-29569200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:29564000-29569600	Weak transcription	Fetal Brain Male	brain
44	chr6:29564400-29567600	Weak transcription	NH-A	brain
45	chr6:29564400-29569600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:29564600-29567000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr6:29564600-29567200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:29564600-29567200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:29564800-29566600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:29564800-29567400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links