Variant report

Variant	rs72828059
Chromosome Location	chr17:33943781-33943782
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:33942629..33946842-chr17:33950583..33953394,3	K562	blood:
2	chr17:33936111..33938621-chr17:33942127..33945092,2	K562	blood:
3	chr17:33942997..33945980-chr17:33946523..33950492,3	K562	blood:
4	chr17:33903102..33905242-chr17:33943673..33945209,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12103451	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12103729	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12150473	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12150480	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16971277	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs321600	0.84[ASN][1000 genomes]
rs321602	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34619890	0.85[EUR][1000 genomes]
rs55898431	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56056154	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56227129	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56292300	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61515677	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72828056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72828073	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72828084	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72828093	0.81[EUR][1000 genomes]
rs740913	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9892037	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9892539	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9906309	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9906872	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9908809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909815	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9911836	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 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	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
2	chr17:33916400-33944800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:33916800-33945400	Weak transcription	Stomach Mucosa	stomach
4	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr17:33920600-33944000	Strong transcription	Dnd41	blood
6	chr17:33920600-33969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:33920800-33975800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr17:33921000-33946200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr17:33921000-33946600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:33921800-33944000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr17:33926000-33955200	Weak transcription	Pancreas	Pancrea
13	chr17:33926200-33943800	Weak transcription	Fetal Heart	heart
14	chr17:33926800-33952600	Weak transcription	Fetal Brain Male	brain
15	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:33933000-33967400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:33933000-33997800	Weak transcription	Esophagus	oesophagus
18	chr17:33933600-33952800	Weak transcription	Brain Substantia Nigra	brain
19	chr17:33933600-33967400	Weak transcription	Gastric	stomach
20	chr17:33934200-33945600	Strong transcription	K562	blood
21	chr17:33934400-33944000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr17:33935000-33951400	Weak transcription	Brain Angular Gyrus	brain
23	chr17:33935600-33944200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr17:33935600-33953000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:33935600-33953400	Weak transcription	HSMMtube	muscle
26	chr17:33936000-33953800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr17:33936800-33956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr17:33937000-33951000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr17:33937000-33951400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr17:33937000-33951400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:33937000-33951800	Weak transcription	HepG2	liver
32	chr17:33937200-33947000	Weak transcription	Placenta	Placenta
33	chr17:33937200-33951200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr17:33937200-33951400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr17:33937400-33951400	Weak transcription	Ovary	ovary
36	chr17:33937400-33965000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr17:33938200-33953200	Weak transcription	Colonic Mucosa	Colon
38	chr17:33938400-33951400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:33938600-33945400	Weak transcription	Colon Smooth Muscle	Colon
40	chr17:33938600-33946800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr17:33938600-33950600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr17:33938600-33951000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr17:33938600-33951000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr17:33938600-33951200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr17:33938600-33951400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr17:33938600-33951400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr17:33938600-33951400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr17:33938600-33952000	Weak transcription	Fetal Brain Female	brain
49	chr17:33938600-33952800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr17:33938600-33953400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links