Variant report

Variant	rs66539836
Chromosome Location	chr7:124568160-124568161
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	POLR2A	chr7:124566718-124570402	K562	blood:	n/a	n/a
2	POLR2A	chr7:124567545-124568225	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:124521370..124523136-chr7:124567552..124569550,2	K562	blood:
2	chr7:124534351..124537236-chr7:124567413..124569702,2	K562	blood:

Variant related genes	Relation type
POT1-AS1	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs34065666	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34721371	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35463079	0.86[EUR][1000 genomes]
rs55654359	1.00[EUR][1000 genomes]
rs56135137	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56403870	0.86[EUR][1000 genomes]
rs57593125	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57883866	1.00[EUR][1000 genomes]
rs58372288	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59044225	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59045238	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs59572327	1.00[EUR][1000 genomes]
rs59653477	1.00[EUR][1000 genomes]
rs59802163	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60046069	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60278737	0.86[EUR][1000 genomes]
rs61126904	0.86[EUR][1000 genomes]
rs61504594	0.86[EUR][1000 genomes]
rs61660401	0.86[EUR][1000 genomes]
rs66461856	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66480671	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66501705	0.86[EUR][1000 genomes]
rs66506561	0.86[EUR][1000 genomes]
rs66528014	1.00[EUR][1000 genomes]
rs66578146	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66610287	0.86[EUR][1000 genomes]
rs66639470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66965758	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66979057	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67166441	1.00[EUR][1000 genomes]
rs67326132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67476012	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs67611448	0.86[EUR][1000 genomes]
rs67712588	0.86[EUR][1000 genomes]
rs67985498	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68016764	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs68099817	0.86[EUR][1000 genomes]
rs6954402	0.86[EUR][1000 genomes]
rs73223520	0.86[EUR][1000 genomes]
rs73223522	0.86[EUR][1000 genomes]
rs73223548	0.86[EUR][1000 genomes]
rs73225404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73443852	1.00[EUR][1000 genomes]
rs7801681	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv3446198	chr7:124358002-124586856	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv889135	chr7:124462081-124584834	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv464707	chr7:124486980-124572288	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv608341	chr7:124486980-124572288	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv889137	chr7:124513770-124584834	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv889138	chr7:124518766-124584834	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv608342	chr7:124549573-124600505	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124462200-124568200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr7:124498200-124568800	Weak transcription	Brain Anterior Caudate	brain
3	chr7:124522800-124568400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:124527600-124569000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:124527600-124569000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:124530000-124569000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:124532000-124569000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:124532600-124568400	Weak transcription	NHDF-Ad	bronchial
9	chr7:124532600-124568800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr7:124532600-124569000	Weak transcription	HSMM	muscle
11	chr7:124532800-124568400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:124532800-124569000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr7:124538000-124569200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:124541000-124568600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:124541000-124569000	Weak transcription	Fetal Muscle Leg	muscle
16	chr7:124541400-124568800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:124541400-124568800	Weak transcription	Fetal Intestine Small	intestine
18	chr7:124541400-124569000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:124541400-124569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:124541400-124569000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:124541400-124569400	Weak transcription	Lung	lung
22	chr7:124541600-124569200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr7:124548400-124569000	Weak transcription	NH-A	brain
24	chr7:124550200-124569200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:124550600-124568800	Weak transcription	Fetal Intestine Large	intestine
26	chr7:124550800-124569000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr7:124551000-124569000	Weak transcription	HSMMtube	muscle
28	chr7:124551400-124568800	Weak transcription	Fetal Kidney	kidney
29	chr7:124551800-124568800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:124552400-124569000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:124553200-124568800	Weak transcription	Fetal Thymus	thymus
32	chr7:124553400-124568800	Weak transcription	HMEC	breast
33	chr7:124553800-124568400	Weak transcription	Fetal Lung	lung
34	chr7:124554600-124568600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:124555400-124569000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:124555600-124568400	Weak transcription	Adipose Nuclei	Adipose
37	chr7:124555600-124568800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:124555600-124569000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:124555800-124568800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr7:124557200-124568800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr7:124557400-124568400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:124557400-124569000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:124557600-124568200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:124558200-124568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:124558200-124568800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:124558200-124569200	Weak transcription	Left Ventricle	heart
47	chr7:124559600-124568400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:124560000-124568400	Weak transcription	Ovary	ovary
49	chr7:124560000-124569400	Weak transcription	Small Intestine	intestine
50	chr7:124560200-124568200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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