Variant report

Variant	rs17409602
Chromosome Location	chr7:6116850-6116851
allele	C/T
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	MYC	chr7:6116691-6117213	Hela-S3	cervix:	n/a	n/a
2	ARID3A	chr7:6116652-6117359	HepG2	liver:	n/a	n/a
3	ELF1	chr7:6116815-6117202	A549	lung:	n/a	n/a
4	SP1	chr7:6116531-6117481	A549	lung:	n/a	n/a
5	USF1	chr7:6116726-6117147	A549	lung:	n/a	n/a
6	NR3C1	chr7:6116711-6117323	A549	lung:	n/a	n/a
7	CBX3	chr7:6116699-6117443	HCT-116	colon:	n/a	n/a
8	NFIC	chr7:6116667-6117382	HepG2	liver:	n/a	n/a
9	STAT3	chr7:6116723-6117257	Hela-S3	cervix:	n/a	n/a
10	BHLHE40	chr7:6116766-6117236	HepG2	liver:	n/a	n/a
11	FOSL1	chr7:6116695-6117382	HCT-116	colon:	n/a	n/a
12	NR3C1	chr7:6116793-6117353	A549	lung:	n/a	n/a
13	MAX	chr7:6116700-6117430	HCT-116	colon:	n/a	n/a
14	CEBPB	chr7:6116825-6117513	IMR90	lung:	n/a	n/a
15	SIN3AK20	chr7:6116727-6117392	HCT-116	colon:	n/a	n/a
16	JUND	chr7:6116749-6117197	Hela-S3	cervix:	n/a	chr7:6116964-6116975
17	GABPA	chr7:6116731-6117173	A549	lung:	n/a	n/a
18	TEAD4	chr7:6116720-6117352	HCT-116	colon:	n/a	n/a
19	MAX	chr7:6116681-6117450	A549	lung:	n/a	n/a
20	CTCF	chr7:6116780-6116930	HepG2	liver:	n/a	n/a
21	TEAD4	chr7:6116697-6117375	ECC-1	luminal epithelium:	n/a	n/a
22	TEAD4	chr7:6116733-6117387	ECC-1	luminal epithelium:	n/a	n/a
23	JUND	chr7:6116723-6117327	SK-N-SH	brain:	n/a	chr7:6116964-6116975
24	EP300	chr7:6116653-6117464	A549	lung:	n/a	n/a
25	TCF12	chr7:6116683-6117441	ECC-1	luminal epithelium:	n/a	n/a
26	FOSL1	chr7:6116698-6117448	HCT-116	colon:	n/a	n/a
27	YY1	chr7:6116835-6117221	HCT-116	colon:	n/a	n/a
28	NFIC	chr7:6116696-6117422	ECC-1	luminal epithelium:	n/a	n/a
29	RAD21	chr7:6116809-6117191	HepG2	liver:	n/a	n/a
30	TCF7L2	chr7:6116664-6117364	PANC-1	pancreas:	n/a	chr7:6117025-6117039 chr7:6117046-6117060 chr7:6117007-6117021
31	RCOR1	chr7:6116826-6117333	HepG2	liver:	n/a	n/a
32	MAFK	chr7:6116784-6117271	Hela-S3	cervix:	n/a	n/a
33	TCF7L2	chr7:6116687-6117455	Hela-S3	cervix:	n/a	chr7:6117025-6117039 chr7:6117046-6117060 chr7:6117007-6117021
34	MAX	chr7:6116702-6117325	A549	lung:	n/a	n/a
35	POLR2A	chr7:6116686-6117290	HCT-116	colon:	n/a	n/a
36	RCOR1	chr7:6116642-6117360	Hela-S3	cervix:	n/a	n/a
37	TCF12	chr7:6116589-6117480	ECC-1	luminal epithelium:	n/a	n/a
38	TFAP2A	chr7:6116835-6117373	Hela-S3	cervix:	n/a	n/a
39	EP300	chr7:6116699-6117481	ECC-1	luminal epithelium:	n/a	n/a
40	TCF7L2	chr7:6116719-6117200	HepG2	liver:	n/a	chr7:6117025-6117039 chr7:6117046-6117060 chr7:6117007-6117021
41	NR2F2	chr7:6116749-6117379	HepG2	liver:	n/a	n/a
42	TCF7L2	chr7:6116689-6117448	HCT-116	colon:	n/a	chr7:6117025-6117039 chr7:6117046-6117060 chr7:6117007-6117021
43	MXI1	chr7:6116779-6117308	HepG2	liver:	n/a	n/a
44	FOSL2	chr7:6116685-6117457	HepG2	liver:	n/a	chr7:6116963-6116974
45	CTCF	chr7:6116700-6116850	HEK293	kidney:	n/a	n/a
46	FOSL2	chr7:6116727-6117324	SK-N-SH	brain:	n/a	chr7:6116963-6116974
47	FOXA2	chr7:6116538-6117155	A549	lung:	n/a	n/a
48	PRDM1	chr7:6116725-6117314	Hela-S3	cervix:	n/a	chr7:6116894-6116908
49	CEBPB	chr7:6116697-6117448	HCT-116	colon:	n/a	n/a
50	FOXM1	chr7:6116683-6117392	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6115370..6118556-chr7:6119697..6122201,4	MCF-7	breast:
2	chr7:6115420..6117338-chr7:6120602..6122627,2	K562	blood:
3	chr7:6090422..6101465-chr7:6116449..6124326,16	K562	blood:
4	chr7:6098532..6100576-chr7:6116384..6118671,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231704	TF binding region
ENSG00000252929	Chromatin interaction
ENSG00000231704	Chromatin interaction
ENSG00000086232	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10230572	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35814282	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66962214	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6958678	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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	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
13	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
14	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
15	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
16	nsv5628	chr7:6105462-6147148	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17409602	EIF2AK1	cis	cerebellum	SCAN
rs17409602	EIF2AK1	cis	parietal	SCAN
rs17409602	JTV1	cis	multi-tissue	Pritchard
rs17409602	PMS2	cis	cerebellum	SCAN
rs17409602	EIF2AK1	Cis_1M	lymphoblastoid	RTeQTL
rs17409602	EIF2AK1	cis	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6111400-6119800	Weak transcription	K562	blood
2	chr7:6114600-6117000	Weak transcription	Adipose Nuclei	Adipose
3	chr7:6114600-6120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:6115000-6117000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr7:6115200-6118200	Weak transcription	Primary B cells from cord blood	blood
6	chr7:6115800-6117800	Enhancers	Placenta	Placenta
7	chr7:6116600-6117400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:6116600-6117600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:6116600-6117600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:6116600-6117600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:6116600-6117600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:6116600-6117600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:6116600-6117600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr7:6116600-6117600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:6116600-6117600	Flanking Active TSS	Hela-S3	cervix
16	chr7:6116600-6117600	Flanking Active TSS	HepG2	liver
17	chr7:6116600-6117800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr7:6116600-6118000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr7:6116800-6117000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:6116800-6117000	Active TSS	A549	lung
21	chr7:6116800-6117200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:6116800-6117200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:6116800-6117400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:6116800-6117400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr7:6116800-6117400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:6116800-6117600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:6116800-6117600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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