Variant report

Variant	rs13163671
Chromosome Location	chr5:177546990-177546991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57921588..57924164-chr5:177545029..177548240,3	MCF-7	breast:
2	chr5:177545145..177547766-chr5:177633548..177635586,2	K562	blood:
3	chr5:177544302..177547027-chr5:177629506..177633017,3	K562	blood:
4	chr5:177546904..177549875-chr5:177630412..177633087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197451	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10035478	0.85[ASN][1000 genomes]
rs10040895	0.83[EUR][1000 genomes]
rs10060446	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12655707	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13155699	0.81[ASN][1000 genomes]
rs13165989	0.84[ASN][1000 genomes]
rs13175750	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13180226	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13185763	0.82[ASN][1000 genomes]
rs13436876	0.85[ASN][1000 genomes]
rs34093388	0.92[ASN][1000 genomes]
rs34343747	0.82[ASN][1000 genomes]
rs34353050	0.84[ASN][1000 genomes]
rs34882864	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35433113	0.82[ASN][1000 genomes]
rs35450829	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35598853	0.83[ASN][1000 genomes]
rs36087128	0.82[ASN][1000 genomes]
rs36090803	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812073	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812074	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812075	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812077	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812079	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924305	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4637566	0.85[ASN][1000 genomes]
rs56351116	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6601217	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7447860	0.85[ASN][1000 genomes]
rs7716409	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7716860	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7733574	0.81[ASN][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	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv883186	chr5:177376317-177549491	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active 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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
4	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv600391	chr5:177488281-177549491	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
7	nsv462567	chr5:177505021-177572927	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv471058	chr5:177505021-177572927	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv600392	chr5:177505021-177572927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
11	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv883191	chr5:177535370-177551985	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
13	nsv883192	chr5:177535370-177564346	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 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	chr5:177541800-177557200	Weak transcription	Right Atrium	heart
2	chr5:177542000-177549600	Enhancers	Primary hematopoietic stem cells	blood
3	chr5:177542200-177547000	Weak transcription	NHEK	skin
4	chr5:177542400-177547000	Enhancers	Spleen	Spleen
5	chr5:177542600-177551000	Weak transcription	Gastric	stomach
6	chr5:177543000-177547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:177543800-177547000	Enhancers	HUVEC	blood vessel
8	chr5:177543800-177548400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:177544200-177548200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr5:177544400-177548200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr5:177544400-177548200	Weak transcription	Pancreas	Pancrea
12	chr5:177544400-177549200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr5:177544600-177547800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:177544600-177547800	Weak transcription	Fetal Intestine Small	intestine
15	chr5:177544600-177552200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:177544800-177547600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:177545000-177547400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:177545000-177547600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:177545000-177547600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:177545200-177547400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:177545200-177547600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
22	chr5:177545200-177552000	Enhancers	Fetal Thymus	thymus
23	chr5:177545400-177547000	Weak transcription	HSMMtube	muscle
24	chr5:177545400-177547600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:177545400-177547600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:177545400-177547600	Weak transcription	Thymus	Thymus
27	chr5:177545400-177547600	Weak transcription	Dnd41	blood
28	chr5:177545400-177547800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:177545400-177547800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr5:177545400-177548200	Weak transcription	Left Ventricle	heart
31	chr5:177545400-177548600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:177545400-177549800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:177545600-177547000	Weak transcription	Esophagus	oesophagus
34	chr5:177545600-177547400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr5:177545600-177547800	Weak transcription	Primary T cells from cord blood	blood
36	chr5:177545600-177547800	Weak transcription	K562	blood
37	chr5:177545600-177550000	Enhancers	Primary B cells from cord blood	blood
38	chr5:177545800-177547600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:177545800-177547800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:177545800-177548200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:177546200-177548200	Genic enhancers	Fetal Muscle Leg	muscle
42	chr5:177546200-177550000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:177546200-177551400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:177546200-177551800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr5:177546200-177552000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:177546400-177547400	Weak transcription	GM12878-XiMat	blood
47	chr5:177546400-177547600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:177546400-177547800	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr5:177546400-177548000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:177546400-177549400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links