Variant report

Variant	rs62473005
Chromosome Location	chr7:98742510-98742511
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	SRF	chr7:98741949-98742521	ECC-1	luminal epithelium:	n/a	chr7:98742246-98742257 chr7:98742242-98742256 chr7:98742243-98742260 chr7:98742245-98742258 chr7:98742244-98742259
2	SIN3AK20	chr7:98739550-98742535	MCF-7	breast:	n/a	n/a
3	POLR2A	chr7:98740853-98743102	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:98741447-98742753	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr7:98741177-98742549	MCF10A-Er-Src	breast:	n/a	n/a
6	REST	chr7:98740927-98742530	H1-neurons	neurons:	n/a	chr7:98741823-98741836
7	SRF	chr7:98741806-98742543	MCF-7	breast:	n/a	chr7:98742246-98742257 chr7:98742242-98742256 chr7:98742243-98742260 chr7:98742245-98742258 chr7:98742244-98742259
8	POLR2A	chr7:98740639-98742774	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:98742101..98744840-chr7:98747144..98750541,3	K562	blood:
2	chr7:98678288..98682057-chr7:98738982..98742511,4	MCF-7	breast:
3	chr7:98741779..98743305-chr7:98813050..98816035,2	MCF-7	breast:
4	chr7:98739614..98743126-chr7:98922770..98926033,5	MCF-7	breast:
5	chr7:98738526..98746153-chr7:98804876..98809686,18	MCF-7	breast:
6	chr7:98740498..98742801-chr7:98868578..98871943,3	MCF-7	breast:

Variant related genes	Relation type
SMURF1	TF binding region
ENSG00000241685	Chromatin interaction
ENSG00000198742	Chromatin interaction
ENSG00000002079	Chromatin interaction
ENSG00000185467	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10953280	0.96[ASN][1000 genomes]
rs11975761	0.96[ASN][1000 genomes]
rs12531875	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12532625	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12534399	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807885	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28545226	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236540	0.92[ASN][1000 genomes]
rs58450802	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62472984	0.96[ASN][1000 genomes]
rs62473003	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62473006	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62473007	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62473008	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62473009	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62473010	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62473011	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62473013	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62473015	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62473048	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62473051	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6954584	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6956283	0.84[ASN][1000 genomes]
rs6958790	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6969140	1.00[ASN][1000 genomes]
rs9297145	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024529	chr7:98194830-98793518	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539036	chr7:98194830-98793518	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv2755119	chr7:98721885-98800145	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	esv1792421	chr7:98737119-98752081	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
5	esv3370738	chr7:98739216-98743614	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
6	esv3348105	chr7:98740041-98742664	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	esv3341751	chr7:98740041-98742989	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98738800-98742600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:98739000-98742600	Active TSS	Rectal Smooth Muscle	rectum
3	chr7:98739200-98743200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:98739400-98742600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr7:98739600-98742600	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr7:98739600-98742600	Active TSS	Fetal Intestine Large	intestine
7	chr7:98739600-98742600	Active TSS	Fetal Kidney	kidney
8	chr7:98739800-98742600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr7:98740000-98742600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:98740000-98742600	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr7:98740000-98742600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr7:98740000-98742600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr7:98740000-98742600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:98740600-98742600	Active TSS	Primary T cells from cord blood	blood
15	chr7:98740600-98742600	Active TSS	Brain Germinal Matrix	brain
16	chr7:98741800-98742600	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr7:98741800-98742600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr7:98742000-98742600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:98742000-98742600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr7:98742000-98742600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr7:98742000-98742600	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr7:98742000-98742600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr7:98742000-98742600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr7:98742000-98742600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:98742000-98742600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:98742000-98742600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr7:98742000-98742600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:98742000-98742600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr7:98742000-98742600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr7:98742000-98742600	Flanking Active TSS	Fetal Brain Female	brain
31	chr7:98742000-98742600	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr7:98742000-98742600	Flanking Active TSS	Fetal Thymus	thymus
33	chr7:98742000-98742600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr7:98742000-98742600	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr7:98742000-98742600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr7:98742000-98742800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:98742000-98742800	Flanking Active TSS	Dnd41	blood
38	chr7:98742200-98742600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:98742200-98742600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr7:98742200-98742600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr7:98742200-98742600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr7:98742200-98742600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr7:98742200-98742600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:98742200-98742600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:98742200-98742600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:98742200-98742600	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr7:98742200-98742600	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr7:98742200-98742600	Flanking Active TSS	Colonic Mucosa	Colon
49	chr7:98742200-98742600	Flanking Active TSS	Fetal Stomach	stomach
50	chr7:98742200-98742600	Flanking Active TSS	Thymus	Thymus

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