Variant report

Variant	rs519611
Chromosome Location	chr7:6095554-6095555
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:6095549-6095586	HepG2	liver:	n/a	n/a
2	RPC155	chr7:6095245-6095728	Hela-S3	cervix:	n/a	n/a
3	FOXA1	chr7:6094992-6095562	HepG2	liver:	n/a	chr7:6095277-6095289
4	ZNF384	chr7:6095004-6096750	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6094946..6099638-chr7:6140891..6146239,12	K562	blood:
2	chr7:6089956..6092329-chr7:6093518..6095916,2	K562	blood:
3	chr7:6062377..6067234-chr7:6094768..6099711,6	K562	blood:
4	chr7:6094663..6096735-chr7:6097687..6100252,2	MCF-7	breast:
5	chr7:6076544..6078828-chr7:6094405..6095983,2	K562	blood:
6	chr7:6093766..6095799-chr7:6101650..6104432,2	MCF-7	breast:
7	chr7:6094497..6101614-chr7:6140891..6145784,14	K562	blood:
8	chr7:6047930..6051239-chr7:6095534..6098918,6	K562	blood:
9	chr7:6090422..6101465-chr7:6116449..6124326,16	K562	blood:

No data

Variant related genes	Relation type
RNU6-218P	TF binding region
ENSG00000086232	Chromatin interaction
ENSG00000106305	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000231704	Chromatin interaction
ENSG00000264605	Chromatin interaction
ENSG00000106346	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10245987	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10249759	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10252733	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10253000	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10254125	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10263017	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11766558	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11766581	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11770056	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11770075	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2302332	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs509228	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs525090	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs533575	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs543770	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs559842	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs590976	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6463527	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs672221	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6959042	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7777896	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs852148	0.82[AFR][1000 genomes]
rs9640012	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[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
rs519611	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	chr7:6050000-6097800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6071600-6097200	Weak transcription	Right Atrium	heart
5	chr7:6076000-6097800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:6083200-6097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:6083600-6097200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:6084400-6096400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:6084400-6098200	Weak transcription	Esophagus	oesophagus
10	chr7:6085000-6096600	Weak transcription	HUVEC	blood vessel
11	chr7:6085200-6097200	Weak transcription	Psoas Muscle	Psoas
12	chr7:6085400-6097000	Weak transcription	Colon Smooth Muscle	Colon
13	chr7:6086000-6098200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:6086200-6097000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:6086400-6096400	Weak transcription	NHDF-Ad	bronchial
16	chr7:6086800-6097600	Weak transcription	Fetal Kidney	kidney
17	chr7:6087000-6096600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:6087600-6097000	Weak transcription	HSMMtube	muscle
19	chr7:6087600-6097200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:6087600-6097200	Weak transcription	Small Intestine	intestine
21	chr7:6088200-6097000	Weak transcription	HSMM	muscle
22	chr7:6088800-6096600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:6088800-6096800	Weak transcription	HMEC	breast
24	chr7:6089000-6096800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr7:6089000-6097000	Weak transcription	Brain Angular Gyrus	brain
26	chr7:6089000-6097000	Weak transcription	Fetal Brain Male	brain
27	chr7:6089200-6096600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:6089200-6097000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:6089200-6097000	Weak transcription	Fetal Lung	lung
30	chr7:6089400-6096400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:6089400-6097000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr7:6089400-6097600	Weak transcription	Right Ventricle	heart
33	chr7:6089400-6097800	Weak transcription	Left Ventricle	heart
34	chr7:6090800-6096400	Weak transcription	Fetal Heart	heart
35	chr7:6091400-6097200	Weak transcription	Gastric	stomach
36	chr7:6092600-6095800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:6092600-6096600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:6092800-6097000	Weak transcription	NH-A	brain
39	chr7:6093000-6097200	Weak transcription	Colonic Mucosa	Colon
40	chr7:6094200-6096400	Weak transcription	Primary T cells from cord blood	blood
41	chr7:6094200-6096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:6094200-6097000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr7:6094200-6097200	Weak transcription	Fetal Brain Female	brain
44	chr7:6094200-6097600	Weak transcription	Brain Substantia Nigra	brain
45	chr7:6094400-6096400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:6094400-6096400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:6094400-6096400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr7:6094400-6096600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr7:6094400-6096600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr7:6094400-6096600	Weak transcription	Ovary	ovary

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