Variant report

Variant	rs73058621
Chromosome Location	chr7:6143625-6143626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:6143393-6143821	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr7:6142253-6143715	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:6143519-6143653	A549	lung:	n/a	n/a
4	POLR2A	chr7:6143372-6143846	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr7:6143264-6143693	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:6142181-6143703	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr7:6143228-6143773	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr7:6142086-6143833	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:6143041-6143811	K562	blood:	n/a	n/a
10	POLR2A	chr7:6143378-6143702	GM12892	blood:	n/a	n/a
11	POLR2A	chr7:6143565-6143742	Hela-S3	cervix:	n/a	n/a
12	HEY1	chr7:6143353-6143733	HepG2	liver:	n/a	n/a
13	POLR2A	chr7:6143000-6143773	K562	blood:	n/a	n/a
14	POLR2A	chr7:6143544-6143742	GM12878	blood:	n/a	n/a
15	POLR2A	chr7:6143432-6143821	GM12892	blood:	n/a	n/a
16	POLR2A	chr7:6142857-6143833	HL-60	blood:	n/a	n/a
17	POLR2A	chr7:6143528-6144780	GM19193	blood:	n/a	n/a
18	HEY1	chr7:6143071-6143799	K562	blood:	n/a	n/a
19	POLR2A	chr7:6142977-6144904	K562	blood:	n/a	n/a
20	NFYA	chr7:6143535-6144578	Hela-S3	cervix:	n/a	chr7:6144315-6144333 chr7:6144317-6144327 chr7:6144315-6144330 chr7:6144314-6144326 chr7:6144315-6144330 chr7:6144315-6144329
21	POLR2A	chr7:6143450-6143688	Raji	blood:	n/a	n/a
22	HA-E2F1	chr7:6143475-6144507	MCF-7	breast:	n/a	chr7:6144317-6144326
23	HCFC1	chr7:6143424-6144749	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr7:6143074-6143812	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr7:6143611-6143658	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr7:6143548-6144926	MCF-7	breast:	n/a	n/a
27	POLR2A	chr7:6143579-6144716	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr7:6143514-6143800	GM12878	blood:	n/a	n/a
29	POLR2A	chr7:6141885-6144613	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr7:6143172-6143702	MCF-7	breast:	n/a	n/a
31	POLR2A	chr7:6142013-6143811	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr7:6142496-6144764	IMR90	lung:	n/a	n/a
33	POLR2A	chr7:6143463-6143691	HCT-116	colon:	n/a	n/a
34	POLR2A	chr7:6143039-6143771	GM12878	blood:	n/a	n/a
35	GTF3C2	chr7:6143552-6144260	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr7:6143430-6143637	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr7:6142982-6143801	GM12892	blood:	n/a	n/a
38	POLR2A	chr7:6141526-6144821	HepG2	liver:	n/a	n/a
39	POLR2A	chr7:6143572-6143687	MCF-7	breast:	n/a	n/a
40	POLR2A	chr7:6143174-6143825	GM12892	blood:	n/a	n/a
41	POLR2A	chr7:6143292-6144878	Hela-S3	cervix:	n/a	n/a
42	STAT3	chr7:6143509-6143705	MCF10A-Er-Src	breast:	n/a	n/a
43	ELF1	chr7:6143519-6144824	GM12878	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6046967..6050535-chr7:6141219..6149580,10	K562	blood:
2	chr7:6119410..6124898-chr7:6141396..6145150,7	MCF-7	breast:
3	chr7:6064661..6068184-chr7:6142795..6145849,5	MCF-7	breast:
4	chr7:6096872..6099965-chr7:6142845..6147736,5	MCF-7	breast:
5	chr7:6118710..6122632-chr7:6142742..6146844,10	K562	blood:
6	chr7:6055602..6058271-chr7:6142750..6144893,2	MCF-7	breast:
7	chr7:6047404..6049912-chr7:6142714..6146343,4	MCF-7	breast:
8	chr7:6047026..6051403-chr7:6141746..6146462,7	K562	blood:
9	chr7:6100114..6101811-chr7:6141887..6144361,2	K562	blood:
10	chr7:6141805..6147526-chr7:6152442..6159269,12	MCF-7	breast:
11	chr7:6119521..6122293-chr7:6142698..6146719,8	K562	blood:
12	chr2:135675640..135676288-chr7:6143525..6144422,2	Hela-S3	cervix:
13	chr7:6096763..6100631-chr7:6141376..6146373,15	MCF-7	breast:
14	chr7:6065831..6068709-chr7:6141820..6144838,4	MCF-7	breast:
15	chr7:6143403..6145262-chr7:6310829..6313708,2	MCF-7	breast:
16	chr7:6062330..6064601-chr7:6141391..6143688,2	MCF-7	breast:
17	chr7:6094497..6101614-chr7:6140891..6145784,14	K562	blood:
18	chr7:6127500..6130529-chr7:6140681..6143799,3	MCF-7	breast:
19	chr7:6142905..6144683-chr7:6522279..6524664,2	MCF-7	breast:
20	chr7:6118878..6122850-chr7:6140823..6146720,14	MCF-7	breast:
21	chr7:6054346..6056159-chr7:6142852..6144380,2	K562	blood:
22	chr7:6094946..6099638-chr7:6140891..6146239,12	K562	blood:

No data

Variant related genes	Relation type
USP42	TF binding region
ENSG00000231704	Chromatin interaction
ENSG00000082258	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000008256	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000086232	Chromatin interaction
ENSG00000224043	Chromatin interaction
ENSG00000269781	Chromatin interaction
ENSG00000136240	Chromatin interaction
ENSG00000106346	Chromatin interaction
ENSG00000264605	Chromatin interaction
ENSG00000207217	Chromatin interaction
ENSG00000106305	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11535148	0.87[ASN][1000 genomes]
rs11543636	0.87[ASN][1000 genomes]
rs11543689	0.90[ASN][1000 genomes]
rs12672392	0.90[ASN][1000 genomes]
rs3750063	0.90[ASN][1000 genomes]
rs3750064	0.86[ASN][1000 genomes]
rs60977467	0.87[ASN][1000 genomes]
rs62456210	0.83[ASN][1000 genomes]
rs73058616	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs763820	0.87[ASN][1000 genomes]
rs7790350	0.87[ASN][1000 genomes]
rs886676	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
13	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
14	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
15	esv13824	chr7:6123263-6144717	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
16	esv3419592	chr7:6142526-6147024	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	esv3421072	chr7:6143276-6146174	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6139200-6144000	Weak transcription	Spleen	Spleen
2	chr7:6142600-6143800	Flanking Active TSS	Dnd41	blood
3	chr7:6142800-6144400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr7:6143000-6143800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr7:6143200-6143800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:6143200-6143800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:6143200-6143800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:6143200-6143800	Enhancers	Fetal Heart	heart
9	chr7:6143200-6144000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr7:6143200-6144400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:6143200-6144400	Active TSS	A549	lung
12	chr7:6143200-6145200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:6143200-6145600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:6143200-6146200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:6143200-6146200	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr7:6143200-6146200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:6143200-6146400	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr7:6143400-6143800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:6143400-6143800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:6143400-6143800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:6143400-6143800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr7:6143400-6143800	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr7:6143400-6143800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:6143400-6143800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr7:6143400-6143800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr7:6143400-6143800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr7:6143400-6143800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:6143400-6143800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr7:6143400-6143800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:6143400-6143800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr7:6143400-6143800	Flanking Active TSS	Liver	Liver
32	chr7:6143400-6143800	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr7:6143400-6143800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr7:6143400-6143800	Flanking Active TSS	Colonic Mucosa	Colon
35	chr7:6143400-6143800	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr7:6143400-6143800	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr7:6143400-6143800	Flanking Active TSS	Esophagus	oesophagus
38	chr7:6143400-6143800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr7:6143400-6143800	Flanking Active TSS	Fetal Brain Female	brain
40	chr7:6143400-6143800	Flanking Active TSS	Fetal Intestine Large	intestine
41	chr7:6143400-6143800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
42	chr7:6143400-6143800	Enhancers	Fetal Lung	lung
43	chr7:6143400-6143800	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr7:6143400-6143800	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr7:6143400-6143800	Flanking Active TSS	Placenta	Placenta
46	chr7:6143400-6143800	Flanking Active TSS	Fetal Stomach	stomach
47	chr7:6143400-6143800	Flanking Active TSS	Left Ventricle	heart
48	chr7:6143400-6143800	Flanking Active TSS	Pancreas	Pancrea
49	chr7:6143400-6143800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr7:6143400-6143800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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