Variant report

Variant	rs56302473
Chromosome Location	chr7:69066221-69066222
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	WRNIP1	chr7:69065901-69066803	GM12878	blood:	n/a	n/a
2	MXI1	chr7:69060600-69067258	SK-N-SH	brain:	n/a	n/a
3	RUNX3	chr7:69065847-69067042	GM12878	blood:	n/a	chr7:69066855-69066870
4	RUNX3	chr7:69065819-69066235	GM12878	blood:	n/a	n/a
5	CHD2	chr7:69065964-69066235	GM12878	blood:	n/a	n/a
6	MAZ	chr7:69066212-69066402	HepG2	liver:	n/a	n/a
7	MAZ	chr7:69066135-69066331	GM12878	blood:	n/a	n/a
8	CHD1	chr7:69066219-69066779	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:69064794..69066719-chr7:69068260..69070601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234215	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11983891	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12333508	0.80[EUR][1000 genomes]
rs12671695	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1468588	0.80[EUR][1000 genomes]
rs1860488	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1985165	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2098116	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210591	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs210593	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs210596	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs210599	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs210601	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs210604	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs210606	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2533426	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2533427	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2533428	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2533429	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2533430	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2533431	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2533433	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2533435	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2533441	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2533442	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2533444	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2533448	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2533449	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2533451	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2533452	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2533454	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2533455	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2533457	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2533458	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2851483	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2851484	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2851487	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2851489	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851490	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851491	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2851492	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2851496	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2851497	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851498	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2851500	0.80[EUR][1000 genomes]
rs2851501	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851503	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2851504	0.80[EUR][1000 genomes]
rs2851505	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2851506	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2851507	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2851508	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851510	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851511	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851512	0.80[EUR][1000 genomes]
rs2851513	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2851514	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851515	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2851516	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2865116	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3886905	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41849	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41852	0.81[AMR][1000 genomes]
rs4717520	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5005279	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505949	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs513150	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs532820	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs547630	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs565505	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs576193	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs576293	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs585282	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs589983	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs590609	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs593063	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs595681	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs610930	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61135042	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs626767	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs627981	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs645245	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460523	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs646233	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs649200	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6944645	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6974900	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs720056	0.80[EUR][1000 genomes]
rs981291	0.81[EUR][1000 genomes]
rs988282	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv5783	chr7:69048608-69066760	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3340834	chr7:69061816-69066664	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69062000-69066400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:69062000-69066400	Active TSS	Rectal Smooth Muscle	rectum
3	chr7:69062000-69066400	Active TSS	NHDF-Ad	bronchial
4	chr7:69062200-69066800	Active TSS	Brain Anterior Caudate	brain
5	chr7:69064800-69066600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr7:69064800-69066600	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr7:69064800-69067000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:69065000-69066400	Flanking Active TSS	Fetal Muscle Leg	muscle
9	chr7:69065200-69066400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr7:69065200-69066800	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr7:69065200-69067000	Flanking Active TSS	Dnd41	blood
12	chr7:69065400-69066400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr7:69065400-69066400	Active TSS	Fetal Brain Female	brain
14	chr7:69065400-69066400	Weak transcription	Left Ventricle	heart
15	chr7:69065400-69066400	Weak transcription	Lung	lung
16	chr7:69065400-69066600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:69065400-69066600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:69065400-69066800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:69065400-69066800	Flanking Active TSS	Fetal Brain Male	brain
20	chr7:69065400-69069600	Weak transcription	Spleen	Spleen
21	chr7:69065400-69071600	Weak transcription	Aorta	Aorta
22	chr7:69065600-69066400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr7:69065600-69066400	Enhancers	Primary B cells from cord blood	blood
24	chr7:69065600-69066400	Flanking Active TSS	Fetal Stomach	stomach
25	chr7:69065600-69066400	Weak transcription	Psoas Muscle	Psoas
26	chr7:69065600-69066600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr7:69065600-69066600	Enhancers	Primary B cells from peripheral blood	blood
28	chr7:69065600-69066600	Flanking Active TSS	Brain Substantia Nigra	brain
29	chr7:69065600-69066800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:69065600-69066800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:69065600-69066800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr7:69065600-69066800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr7:69065800-69066400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:69065800-69066400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
35	chr7:69065800-69066600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:69065800-69066600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:69065800-69066600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:69065800-69066600	Enhancers	Fetal Muscle Trunk	muscle
39	chr7:69065800-69066600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
40	chr7:69065800-69066600	Bivalent Enhancer	Thymus	Thymus
41	chr7:69065800-69066800	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr7:69065800-69066800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr7:69065800-69067000	Enhancers	Right Atrium	heart
44	chr7:69065800-69067400	Enhancers	Fetal Heart	heart
45	chr7:69066000-69066400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:69066000-69066400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:69066000-69066400	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr7:69066000-69066600	Bivalent Enhancer	Fetal Thymus	thymus
49	chr7:69066000-69066600	Flanking Active TSS	Ovary	ovary
50	chr7:69066000-69066800	Enhancers	NH-A	brain

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