Variant report

Variant	rs559842
Chromosome Location	chr7:6097868-6097869
allele	A/C/G/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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6082731..6088079-chr7:6097012..6099885,4	MCF-7	breast:
2	chr7:6094946..6099638-chr7:6140891..6146239,12	K562	blood:
3	chr7:6047262..6048916-chr7:6096593..6098744,2	MCF-7	breast:
4	chr7:6064770..6067105-chr7:6097512..6099982,2	K562	blood:
5	chr7:6096872..6099965-chr7:6142845..6147736,5	MCF-7	breast:
6	chr7:6096078..6098948-chr7:6116857..6121575,6	K562	blood:
7	chr7:6095667..6100309-chr7:6118978..6123029,12	MCF-7	breast:
8	chr7:6062377..6067234-chr7:6094768..6099711,6	K562	blood:
9	chr7:5631641..5634228-chr7:6097200..6099216,2	K562	blood:
10	chr7:6055912..6057708-chr7:6097324..6099828,2	MCF-7	breast:
11	chr7:6096763..6100631-chr7:6141376..6146373,15	MCF-7	breast:
12	chr7:6097184..6100296-chr7:6118283..6122245,9	MCF-7	breast:
13	chr7:6047579..6050679-chr7:6097211..6100186,3	MCF-7	breast:
14	chr7:6094497..6101614-chr7:6140891..6145784,14	K562	blood:
15	chr7:6047930..6051239-chr7:6095534..6098918,6	K562	blood:
16	chr7:6048500..6051239-chr7:6096959..6099959,3	K562	blood:
17	chr7:6097568..6100190-chr7:6387069..6389785,3	MCF-7	breast:
18	chr7:6090422..6101465-chr7:6116449..6124326,16	K562	blood:

No data

Variant related genes	Relation type
ENSG00000106346	Chromatin interaction
ENSG00000240718	Chromatin interaction
ENSG00000106305	Chromatin interaction
ENSG00000075618	Chromatin interaction
ENSG00000207217	Chromatin interaction
ENSG00000264605	Chromatin interaction
ENSG00000178397	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000231704	Chromatin interaction
ENSG00000086232	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10245987	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10249759	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10252733	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10253000	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10254125	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10263017	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11766558	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11766581	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11770056	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11770075	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2302331	0.85[AFR][1000 genomes]
rs2302332	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509228	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs511969	0.83[AFR][1000 genomes]
rs519611	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs523254	0.87[AFR][1000 genomes]
rs525090	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs533575	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs543770	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs550831	0.84[AFR][1000 genomes]
rs590976	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs607628	0.87[AFR][1000 genomes]
rs6463527	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs672221	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6959042	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7777896	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9640012	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
3	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
5	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
7	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
8	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
9	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
10	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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
11	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
12	nsv605998	chr7:6035065-6102034	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv1018388	chr7:6038713-6131169	Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers 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	58 gene(s)	inside rSNPs	diseases
14	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
15	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
16	esv3405881	chr7:6087760-6122016	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs559842	EIF2AK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6049400-6098000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:6084400-6098200	Weak transcription	Esophagus	oesophagus
3	chr7:6086000-6098200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6095400-6099400	Active TSS	K562	blood
5	chr7:6096400-6099200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:6096400-6099200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr7:6096600-6098000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:6096600-6098000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:6096600-6098000	Active TSS	HepG2	liver
10	chr7:6096600-6098400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:6096800-6098000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr7:6096800-6099000	Active TSS	HMEC	breast
13	chr7:6096800-6099400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr7:6096800-6099400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:6097000-6098000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr7:6097000-6098000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr7:6097000-6098000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr7:6097000-6098000	Enhancers	Primary B cells from peripheral blood	blood
19	chr7:6097000-6098000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr7:6097000-6098000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr7:6097000-6098000	Enhancers	Colon Smooth Muscle	Colon
22	chr7:6097000-6098000	Enhancers	Fetal Brain Male	brain
23	chr7:6097000-6098000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr7:6097000-6098200	Flanking Active TSS	NH-A	brain
25	chr7:6097000-6098600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:6097000-6098600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:6097000-6098600	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr7:6097000-6099000	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr7:6097000-6099200	Active TSS	Placenta	Placenta
30	chr7:6097000-6099400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:6097000-6099400	Active TSS	Fetal Stomach	stomach
32	chr7:6097000-6099400	Active TSS	NHLF	lung
33	chr7:6097200-6098000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:6097200-6098000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:6097200-6098000	Enhancers	Brain Anterior Caudate	brain
36	chr7:6097200-6098000	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr7:6097200-6098000	Enhancers	Lung	lung
38	chr7:6097200-6098000	Enhancers	Small Intestine	intestine
39	chr7:6097200-6098000	Flanking Active TSS	Dnd41	blood
40	chr7:6097200-6098000	Flanking Active TSS	HUVEC	blood vessel
41	chr7:6097200-6098200	Enhancers	Spleen	Spleen
42	chr7:6097200-6098400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr7:6097200-6099200	Active TSS	H9 Cell Line	embryonic stem cell
44	chr7:6097200-6099200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:6097200-6099200	Active TSS	Gastric	stomach
46	chr7:6097200-6099400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:6097200-6099400	Active TSS	A549	lung
48	chr7:6097200-6099400	Active TSS	HSMM	muscle
49	chr7:6097400-6098000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr7:6097400-6098200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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