Variant report

Variant	rs28494836
Chromosome Location	chr5:176955228-176955229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:176953962..176956873-chr5:176957171..176958842,2	MCF-7	breast:
2	chr5:176950068..176952116-chr5:176953675..176955274,2	MCF-7	breast:
3	chr5:176954396..176956242-chr5:176959292..176962500,4	K562	blood:
4	chr5:176954037..176957185-chr5:176977756..176983051,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146067	Chromatin interaction
ENSG00000272459	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs28366804	1.00[YRI][hapmap]
rs28379386	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28392715	1.00[AMR][1000 genomes]
rs28396982	1.00[AMR][1000 genomes]
rs28464438	1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28483466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28491669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28565502	0.84[AFR][1000 genomes]
rs28587302	1.00[AMR][1000 genomes]
rs28613023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28615269	1.00[AMR][1000 genomes]
rs28630512	0.94[AFR][1000 genomes]
rs28688891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28723606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs337387	1.00[AMR][1000 genomes]
rs337399	1.00[AMR][1000 genomes]
rs388783	1.00[AMR][1000 genomes]
rs4976650	1.00[AMR][1000 genomes]
rs5013573	1.00[AMR][1000 genomes]
rs58021881	1.00[AMR][1000 genomes]
rs6600953	1.00[AMR][1000 genomes]
rs7444245	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	nsv883161	chr5:176754722-176958397	Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv883164	chr5:176780545-177003616	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	esv1816147	chr5:176787037-176966509	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
6	nsv883177	chr5:176868358-177003616	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
8	nsv984570	chr5:176923414-176956300	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv5147	chr5:176938196-176983018	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:176944800-176963400	Weak transcription	Right Atrium	heart
2	chr5:176944800-176972800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:176946000-176966200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:176946000-176968000	Strong transcription	Fetal Thymus	thymus
5	chr5:176946000-176970000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:176946200-176966200	Strong transcription	Fetal Brain Female	brain
7	chr5:176946200-176966200	Strong transcription	Fetal Intestine Small	intestine
8	chr5:176946200-176966800	Strong transcription	Fetal Stomach	stomach
9	chr5:176946200-176968000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:176946200-176969800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:176946200-176970200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:176946200-176971000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr5:176946400-176957200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:176946400-176957800	Weak transcription	Fetal Heart	heart
15	chr5:176946400-176960200	Strong transcription	Aorta	Aorta
16	chr5:176946400-176961200	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr5:176946400-176964000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr5:176946400-176964200	Strong transcription	A549	lung
19	chr5:176946400-176965000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:176946400-176966200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:176946400-176966800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:176946400-176966800	Strong transcription	Fetal Lung	lung
23	chr5:176946400-176969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:176946400-176970000	Strong transcription	Thymus	Thymus
25	chr5:176946600-176956400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:176946600-176956600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:176946600-176960800	Strong transcription	Liver	Liver
28	chr5:176946600-176961800	Strong transcription	Colon Smooth Muscle	Colon
29	chr5:176946600-176962400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:176946600-176963000	Strong transcription	Colonic Mucosa	Colon
31	chr5:176946600-176963800	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:176946600-176963800	Strong transcription	Osteobl	bone
33	chr5:176946600-176965200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:176946600-176966400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:176946600-176966600	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr5:176946600-176966800	Strong transcription	Fetal Intestine Large	intestine
37	chr5:176946600-176969800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:176946800-176957200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:176946800-176963400	Strong transcription	Placenta	Placenta
40	chr5:176946800-176963600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:176946800-176963800	Strong transcription	NHLF	lung
42	chr5:176946800-176967600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:176946800-176977200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:176947000-176966200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr5:176947000-176979000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:176947200-176963400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:176947400-176966200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:176948000-176956200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:176948000-176957000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:176948000-176968000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links