Variant report

Variant	rs672716
Chromosome Location	chr7:6093127-6093128
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:6092882-6093190	K562	blood:	n/a	n/a
2	POLR2A	chr7:6093104-6093136	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:6092890-6093177	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6088385..6094531-chr7:6095693..6100506,11	MCF-7	breast:
2	chr7:6090785..6094392-chr7:6095992..6098375,4	K562	blood:
3	chr7:6090422..6101465-chr7:6116449..6124326,16	K562	blood:

Variant related genes	Relation type
RNU6-218P	TF binding region
ENSG00000264605	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000086232	Chromatin interaction
ENSG00000231704	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2302331	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2345055	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3847023	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511969	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523254	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550831	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607628	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs852148	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9655492	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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
rs672716	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	chr7:6050400-6095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:6050800-6095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:6051000-6095200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr7:6052600-6094600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:6053000-6095000	Strong transcription	Fetal Intestine Small	intestine
9	chr7:6054400-6095200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:6056400-6095200	Strong transcription	Dnd41	blood
11	chr7:6056600-6095200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:6056800-6094800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:6066600-6094600	Strong transcription	Fetal Muscle Leg	muscle
14	chr7:6066800-6094800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:6066800-6095200	Strong transcription	Fetal Thymus	thymus
16	chr7:6067000-6094600	Strong transcription	Placenta	Placenta
17	chr7:6067800-6095200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr7:6068000-6094400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr7:6071000-6094600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr7:6071600-6097200	Weak transcription	Right Atrium	heart
21	chr7:6072600-6095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:6076000-6097800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:6083200-6097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:6083600-6097200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:6084400-6093600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr7:6084400-6096400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr7:6084400-6098200	Weak transcription	Esophagus	oesophagus
28	chr7:6084600-6093800	Weak transcription	NHLF	lung
29	chr7:6085000-6094000	Weak transcription	Aorta	Aorta
30	chr7:6085000-6096600	Weak transcription	HUVEC	blood vessel
31	chr7:6085200-6095000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:6085200-6097200	Weak transcription	Psoas Muscle	Psoas
33	chr7:6085400-6093800	Weak transcription	NHEK	skin
34	chr7:6085400-6097000	Weak transcription	Colon Smooth Muscle	Colon
35	chr7:6086000-6093600	Weak transcription	Spleen	Spleen
36	chr7:6086000-6098200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:6086200-6097000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr7:6086400-6096400	Weak transcription	NHDF-Ad	bronchial
39	chr7:6086800-6097600	Weak transcription	Fetal Kidney	kidney
40	chr7:6087000-6096600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr7:6087600-6097000	Weak transcription	HSMMtube	muscle
42	chr7:6087600-6097200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:6087600-6097200	Weak transcription	Small Intestine	intestine
44	chr7:6088200-6095000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:6088200-6097000	Weak transcription	HSMM	muscle
46	chr7:6088800-6094000	Weak transcription	Hela-S3	cervix
47	chr7:6088800-6096600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:6088800-6096800	Weak transcription	HMEC	breast
49	chr7:6089000-6093600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:6089000-6093800	Weak transcription	Brain Anterior Caudate	brain

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