Variant report

Variant	rs8042601
Chromosome Location	chr15:59404108-59404109
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59403972..59405479-chr15:59405925..59407716,2	K562	blood:
2	chr15:59385316..59387666-chr15:59401206..59404506,4	K562	blood:

Variant related genes	Relation type
ENSG00000157450	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10518998	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574500	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11574501	0.94[EUR][1000 genomes]
rs13498	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16940958	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16940976	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16941012	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16941048	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941077	0.88[EUR][1000 genomes]
rs28383495	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28739021	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28739025	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57164516	0.88[EUR][1000 genomes]
rs6494052	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6494058	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6494067	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7164061	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7171252	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7173787	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7173999	0.94[EUR][1000 genomes]
rs7174992	0.82[EUR][1000 genomes]
rs7175697	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7177112	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7180666	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7181728	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74017367	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8026039	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8027376	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8030514	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8030811	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8032299	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8035952	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8040605	0.86[AMR][1000 genomes]
rs8041633	1.00[AMR][1000 genomes];0.94[EUR][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59397800-59415600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:59397800-59450000	Weak transcription	Small Intestine	intestine
3	chr15:59398000-59407200	Weak transcription	Stomach Mucosa	stomach
4	chr15:59398000-59409600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:59398000-59412200	Weak transcription	Spleen	Spleen
6	chr15:59398000-59423200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:59398000-59423400	Weak transcription	Esophagus	oesophagus
8	chr15:59398000-59425600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:59398000-59426000	Weak transcription	Lung	lung
10	chr15:59398000-59426200	Weak transcription	HSMMtube	muscle
11	chr15:59398000-59426400	Weak transcription	Left Ventricle	heart
12	chr15:59398000-59427200	Weak transcription	Pancreas	Pancrea
13	chr15:59398000-59427400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:59398000-59462000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:59398200-59408600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:59398200-59409400	Weak transcription	Primary B cells from cord blood	blood
17	chr15:59398200-59410400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:59398200-59415200	Weak transcription	Colonic Mucosa	Colon
19	chr15:59398200-59423800	Weak transcription	Fetal Brain Male	brain
20	chr15:59398400-59406600	Weak transcription	Fetal Kidney	kidney
21	chr15:59398400-59407000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:59398400-59408600	Weak transcription	Primary T cells from cord blood	blood
23	chr15:59398400-59409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:59398400-59409200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:59398400-59409400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:59398600-59406600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:59398600-59409200	Weak transcription	Brain Germinal Matrix	brain
28	chr15:59398600-59422600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:59398800-59405800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:59399200-59417600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:59399200-59419600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:59399200-59420200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:59399200-59421600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:59399400-59404400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:59399400-59404600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:59399400-59404800	Strong transcription	A549	lung
37	chr15:59399400-59404800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr15:59399400-59413800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:59399400-59417400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:59399400-59418800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:59399400-59419600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:59399600-59404200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:59399600-59404400	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr15:59399600-59404400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:59399600-59410600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr15:59399600-59413200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:59399600-59413400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:59399600-59413400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:59399600-59419600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:59399600-59437000	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links