Variant report

Variant	rs72924342
Chromosome Location	chr6:88389732-88389733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:88386476..88391429-chr6:88407886..88413024,9	MCF-7	breast:
2	chr6:88387463..88390182-chr6:88429008..88431240,2	MCF-7	breast:
3	chr6:88381197..88391198-chr6:88407466..88413401,14	K562	blood:
4	chr6:88388778..88396986-chr6:88407117..88413072,10	K562	blood:
5	chr6:88389328..88391908-chr6:88403558..88405512,2	K562	blood:
6	chr6:88388879..88390685-chr6:88392735..88395490,2	MCF-7	breast:
7	chr6:88389146..88392060-chr6:88395023..88397672,4	K562	blood:
8	chr6:88389328..88391908-chr6:88402227..88405512,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238628	Chromatin interaction
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs16879704	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16879736	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28381470	0.81[EUR][1000 genomes]
rs28381475	0.81[EUR][1000 genomes]
rs28381530	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3763177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273297	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55909105	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs55985738	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56400749	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57573658	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58060521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59131518	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59774543	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60082015	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60316099	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66502414	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66588280	0.89[EUR][1000 genomes]
rs66965134	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67575319	0.89[EUR][1000 genomes]
rs67700862	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67956402	0.81[EUR][1000 genomes]
rs67993159	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68082038	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6907107	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6932733	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs715207	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72906514	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72922577	0.81[EUR][1000 genomes]
rs72924341	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73498106	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7747792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7748286	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7752473	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7769144	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7776049	0.89[EUR][1000 genomes]
rs9450782	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
5	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
7	chr6:88349400-88397400	Weak transcription	Ovary	ovary
8	chr6:88358200-88392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:88363200-88395000	Weak transcription	Stomach Mucosa	stomach
11	chr6:88365000-88390000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:88366400-88390000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:88366600-88390000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:88368000-88393400	Weak transcription	Small Intestine	intestine
15	chr6:88370200-88391800	Weak transcription	Fetal Brain Male	brain
16	chr6:88372600-88392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:88374200-88391400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:88376400-88390000	Strong transcription	Primary B cells from cord blood	blood
19	chr6:88376600-88390000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:88376800-88389800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:88380400-88390000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:88380400-88391000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:88380600-88391400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:88380800-88390000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr6:88380800-88392400	Strong transcription	Fetal Thymus	thymus
26	chr6:88381000-88390000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:88381000-88391400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr6:88381000-88391600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:88381200-88391600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:88381200-88391800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:88381400-88389800	Strong transcription	Dnd41	blood
32	chr6:88381400-88391400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:88381400-88400600	Weak transcription	Right Atrium	heart
34	chr6:88381600-88390000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:88381600-88392000	Weak transcription	Aorta	Aorta
36	chr6:88381800-88392000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:88382000-88391000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:88382200-88391600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:88382400-88390400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:88382400-88391800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:88382800-88390200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:88383000-88390000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:88383200-88392200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr6:88383600-88391600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:88383800-88390000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr6:88384600-88392200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:88384800-88391000	Strong transcription	Fetal Intestine Large	intestine
48	chr6:88385000-88390800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:88385400-88390000	Weak transcription	Psoas Muscle	Psoas
50	chr6:88385400-88390200	Strong transcription	Adipose Nuclei	Adipose

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