Variant report

Variant	rs61822767
Chromosome Location	chr1:175981458-175981459
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	chr1:175981400-175981498	Gliobla	brain:	n/a	n/a
2	POLR2A	chr1:175981359-175981490	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175980073..175982418-chr1:175990333..175992819,2	K562	blood:

Variant related genes	Relation type
ENSG00000228686	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10436864	0.82[EUR][1000 genomes]
rs10494499	0.88[AMR][1000 genomes]
rs10798427	0.88[EUR][1000 genomes]
rs10798428	0.88[EUR][1000 genomes]
rs11576862	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580753	1.00[ASN][1000 genomes]
rs11583071	1.00[ASN][1000 genomes]
rs11584481	1.00[ASN][1000 genomes]
rs11588480	1.00[ASN][1000 genomes]
rs11590045	1.00[ASN][1000 genomes]
rs12038027	0.86[EUR][1000 genomes]
rs12403794	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12404181	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357337	0.86[EUR][1000 genomes]
rs17351808	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351933	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17352072	0.88[AMR][1000 genomes]
rs17354252	0.88[AMR][1000 genomes]
rs2481647	0.84[EUR][1000 genomes]
rs2481651	0.86[EUR][1000 genomes]
rs2481657	0.86[EUR][1000 genomes]
rs2502822	0.86[EUR][1000 genomes]
rs2502826	0.86[EUR][1000 genomes]
rs2861630	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129061	0.86[EUR][1000 genomes]
rs4307526	0.91[EUR][1000 genomes]
rs4314844	0.91[EUR][1000 genomes]
rs4460596	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4601543	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051510	1.00[ASN][1000 genomes]
rs56198111	1.00[ASN][1000 genomes]
rs56949697	1.00[ASN][1000 genomes]
rs60719126	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60964243	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61186664	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820965	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820968	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820999	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61821007	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821009	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821028	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61822662	0.88[AMR][1000 genomes]
rs6425368	0.88[EUR][1000 genomes]
rs6680309	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693947	0.88[AMR][1000 genomes]
rs6704509	0.91[EUR][1000 genomes]
rs74127150	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74127154	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74127185	0.85[AMR][1000 genomes]
rs7517351	0.84[EUR][1000 genomes]
rs7524972	0.86[EUR][1000 genomes]
rs7537435	0.84[EUR][1000 genomes]
rs7545043	0.87[EUR][1000 genomes]
rs7545639	0.91[EUR][1000 genomes]
rs7552181	0.84[EUR][1000 genomes]
rs7554913	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9783047	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175946000-175996000	Weak transcription	HMEC	breast
2	chr1:175953800-175999600	Weak transcription	Colonic Mucosa	Colon
3	chr1:175954000-175987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:175958000-175987800	Weak transcription	Fetal Thymus	thymus
6	chr1:175973600-176003400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:175974000-176003000	Weak transcription	NH-A	brain
8	chr1:175974400-175988200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:175974600-175981800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:175974600-175988800	Weak transcription	Pancreas	Pancrea
11	chr1:175974600-176014200	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:175975400-176003400	Weak transcription	NHLF	lung
13	chr1:175975600-175988400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:175975800-175988800	Weak transcription	Ovary	ovary
15	chr1:175975800-176016200	Weak transcription	HSMMtube	muscle
16	chr1:175976000-175981600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:175976400-175996000	Weak transcription	HUVEC	blood vessel
18	chr1:175976400-176014400	Weak transcription	Brain Angular Gyrus	brain
19	chr1:175976600-176009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:175977400-175982200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:175977600-175988000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:175978200-175985200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:175978200-175985200	Weak transcription	Fetal Heart	heart
25	chr1:175978200-176001000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:175978200-176003600	Weak transcription	Small Intestine	intestine
27	chr1:175978200-176007400	Weak transcription	Brain Germinal Matrix	brain
28	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
29	chr1:175978400-175981600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:175978400-175984400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:175978400-175985000	Weak transcription	GM12878-XiMat	blood
32	chr1:175978400-175986800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:175978400-175987800	Weak transcription	Fetal Stomach	stomach
34	chr1:175978400-175988000	Weak transcription	Thymus	Thymus
35	chr1:175978400-175988600	Weak transcription	Esophagus	oesophagus
36	chr1:175978400-175989400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:175978400-175996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:175978400-175996600	Weak transcription	Left Ventricle	heart
39	chr1:175978400-176001600	Weak transcription	Fetal Lung	lung
40	chr1:175978400-176003000	Weak transcription	HSMM	muscle
41	chr1:175978400-176006800	Weak transcription	Fetal Brain Female	brain
42	chr1:175978400-176007000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:175978400-176007000	Weak transcription	Fetal Kidney	kidney
44	chr1:175978400-176014000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:175978400-176014800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:175978400-176017800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:175978600-175982400	Strong transcription	Primary B cells from cord blood	blood
49	chr1:175978600-176007000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:175978800-175986000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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