Variant report

Variant	rs10230572
Chromosome Location	chr7:6117377-6117378
allele	G/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	POLR2A	chr7:6116858-6117421	Hela-S3	cervix:	n/a	n/a
2	SP1	chr7:6116531-6117481	A549	lung:	n/a	n/a
3	CBX3	chr7:6116699-6117443	HCT-116	colon:	n/a	n/a
4	NFIC	chr7:6116667-6117382	HepG2	liver:	n/a	n/a
5	REST	chr7:6116892-6117393	HepG2	liver:	n/a	n/a
6	FOSL1	chr7:6116695-6117382	HCT-116	colon:	n/a	n/a
7	CEBPB	chr7:6117292-6117474	HepG2	liver:	n/a	n/a
8	MAX	chr7:6116700-6117430	HCT-116	colon:	n/a	n/a
9	CEBPB	chr7:6116825-6117513	IMR90	lung:	n/a	n/a
10	SIN3AK20	chr7:6116727-6117392	HCT-116	colon:	n/a	n/a
11	MAX	chr7:6116681-6117450	A549	lung:	n/a	n/a
12	TEAD4	chr7:6116733-6117387	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr7:6116653-6117464	A549	lung:	n/a	n/a
14	TCF12	chr7:6116683-6117441	ECC-1	luminal epithelium:	n/a	n/a
15	FOSL1	chr7:6116698-6117448	HCT-116	colon:	n/a	n/a
16	NFIC	chr7:6116696-6117422	ECC-1	luminal epithelium:	n/a	n/a
17	TCF7L2	chr7:6116687-6117455	Hela-S3	cervix:	n/a	chr7:6117025-6117039 chr7:6117046-6117060 chr7:6117007-6117021
18	TCF12	chr7:6116589-6117480	ECC-1	luminal epithelium:	n/a	n/a
19	EP300	chr7:6116699-6117481	ECC-1	luminal epithelium:	n/a	n/a
20	NR2F2	chr7:6116749-6117379	HepG2	liver:	n/a	n/a
21	TCF7L2	chr7:6116689-6117448	HCT-116	colon:	n/a	chr7:6117025-6117039 chr7:6117046-6117060 chr7:6117007-6117021
22	FOSL2	chr7:6116685-6117457	HepG2	liver:	n/a	chr7:6116963-6116974
23	CEBPB	chr7:6116697-6117448	HCT-116	colon:	n/a	n/a
24	FOXM1	chr7:6116683-6117392	ECC-1	luminal epithelium:	n/a	n/a
25	SP1	chr7:6116693-6117397	HCT-116	colon:	n/a	n/a
26	SIN3AK20	chr7:6116692-6117480	HCT-116	colon:	n/a	n/a
27	NR3C1	chr7:6116735-6117397	A549	lung:	n/a	n/a
28	TBP	chr7:6116727-6117387	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr7:6116761-6117533	HepG2	liver:	n/a	n/a
30	YY1	chr7:6116957-6117427	HepG2	liver:	n/a	n/a
31	SP1	chr7:6116688-6117413	HCT-116	colon:	n/a	n/a
32	EP300	chr7:6116565-6117450	A549	lung:	n/a	n/a
33	CEBPB	chr7:6116748-6117602	A549	lung:	n/a	n/a
34	JUND	chr7:6116532-6117449	SK-N-SH	brain:	n/a	chr7:6116964-6116975
35	GTF3C2	chr7:6116526-6117610	Hela-S3	cervix:	n/a	n/a
36	SP1	chr7:6116526-6117452	A549	lung:	n/a	n/a
37	TEAD4	chr7:6116806-6117420	SK-N-SH	brain:	n/a	n/a
38	CEBPB	chr7:6116690-6117480	HCT-116	colon:	n/a	n/a
39	MYBL2	chr7:6116677-6117573	HepG2	liver:	n/a	n/a
40	CHD1	chr7:6116684-6117607	IMR90	lung:	n/a	n/a
41	MYBL2	chr7:6116577-6117500	HepG2	liver:	n/a	n/a
42	HEY1	chr7:6116767-6117431	HepG2	liver:	n/a	n/a
43	CEBPB	chr7:6116714-6117541	Hela-S3	cervix:	n/a	n/a
44	TBP	chr7:6116767-6117451	HepG2	liver:	n/a	n/a
45	RCOR1	chr7:6116484-6117449	IMR90	lung:	n/a	n/a
46	MAX	chr7:6116710-6117441	HCT-116	colon:	n/a	n/a
47	GATA3	chr7:6116649-6117482	A549	lung:	n/a	n/a
48	JUND	chr7:6116694-6117424	HepG2	liver:	n/a	chr7:6116964-6116975
49	TEAD4	chr7:6116679-6117397	A549	lung:	n/a	n/a
50	TEAD4	chr7:6116688-6117380	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6096078..6098948-chr7:6116857..6121575,6	K562	blood:
2	chr7:6115370..6118556-chr7:6119697..6122201,4	MCF-7	breast:
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
ENSG00000086232	Chromatin interaction
ENSG00000231704	Chromatin interaction
ENSG00000252929	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13230531	0.80[EUR][1000 genomes]
rs13243552	0.80[EUR][1000 genomes]
rs13243604	0.80[EUR][1000 genomes]
rs17409602	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35814282	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66962214	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6958678	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7798319	0.80[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10230572	EIF2AK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6111400-6119800	Weak transcription	K562	blood
2	chr7:6114600-6120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:6115200-6118200	Weak transcription	Primary B cells from cord blood	blood
4	chr7:6115800-6117800	Enhancers	Placenta	Placenta
5	chr7:6116600-6117400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:6116600-6117600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:6116600-6117600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:6116600-6117600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:6116600-6117600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:6116600-6117600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:6116600-6117600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr7:6116600-6117600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:6116600-6117600	Flanking Active TSS	Hela-S3	cervix
14	chr7:6116600-6117600	Flanking Active TSS	HepG2	liver
15	chr7:6116600-6117800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr7:6116600-6118000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr7:6116800-6117400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:6116800-6117400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:6116800-6117400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:6116800-6117600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:6116800-6117600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:6117000-6117400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr7:6117000-6117400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr7:6117000-6117400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:6117000-6117400	Enhancers	Adipose Nuclei	Adipose
26	chr7:6117000-6117400	Enhancers	Esophagus	oesophagus
27	chr7:6117000-6117400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr7:6117000-6117400	Flanking Active TSS	A549	lung
29	chr7:6117000-6117400	Enhancers	NHDF-Ad	bronchial
30	chr7:6117000-6117400	Enhancers	NHLF	lung
31	chr7:6117000-6117600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr7:6117000-6117600	Enhancers	HMEC	breast
33	chr7:6117000-6117600	Enhancers	NHEK	skin
34	chr7:6117000-6117600	Enhancers	Osteobl	bone
35	chr7:6117200-6117400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr7:6117200-6117400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:6117200-6117400	Flanking Active TSS	NH-A	brain
38	chr7:6117200-6117600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:6117200-6117600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr7:6117200-6117600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:6117200-6120000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:6117200-6120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:6117200-6120000	Weak transcription	Brain Substantia Nigra	brain

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