Variant report

Variant	rs61776043
Chromosome Location	chr1:10534567-10534568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10534494-10535668	HepG2	liver:	n/a	n/a
2	STAT1	chr1:10534192-10535148	Hela-S3	cervix:	n/a	chr1:10534835-10534844 chr1:10534833-10534844 chr1:10534834-10534843
3	POLR2A	chr1:10534566-10535680	SK-N-MC	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10533798..10536250-chr1:11072606..11074153,2	MCF-7	breast:
2	chr1:10457403..10461622-chr1:10531171..10536559,7	K562	blood:
3	chr1:10528950..10534210-chr1:10534257..10537658,6	K562	blood:
4	chr1:10489993..10493018-chr1:10531254..10535234,5	MCF-7	breast:
5	chr1:10490607..10494447-chr1:10532445..10535163,5	K562	blood:
6	chr1:10488008..10492443-chr1:10531123..10534892,8	K562	blood:
7	chr1:10364625..10366634-chr1:10534316..10536742,2	K562	blood:
8	chr1:10457843..10460253-chr1:10533493..10537083,3	MCF-7	breast:
9	chr1:10473903..10475499-chr1:10533435..10536154,2	K562	blood:

No data

Variant related genes	Relation type
DFFA	TF binding region
PEX14	TF binding region
ENSG00000271989	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000120948	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000264501	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2274986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663566	0.85[EUR][1000 genomes]
rs57986045	0.86[EUR][1000 genomes]
rs61776015	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61776020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61776039	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61776041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61776042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61776045	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61776260	0.86[EUR][1000 genomes]
rs61776261	0.86[EUR][1000 genomes]
rs61777205	0.86[EUR][1000 genomes]
rs61777209	0.86[EUR][1000 genomes]
rs6540934	0.86[EUR][1000 genomes]
rs6540935	0.86[EUR][1000 genomes]
rs6668910	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6679456	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680568	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534960	0.86[EUR][1000 genomes]
rs7551790	0.86[EUR][1000 genomes]
rs9661820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10532600-10534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:10532600-10534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:10532600-10535000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:10532800-10535000	Weak transcription	Spleen	Spleen
5	chr1:10533000-10534600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:10533000-10534600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:10533000-10534600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:10533000-10534600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:10533000-10534600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:10533000-10534600	Weak transcription	Fetal Brain Female	brain
11	chr1:10533000-10534600	Weak transcription	Left Ventricle	heart
12	chr1:10533000-10534600	Weak transcription	Ovary	ovary
13	chr1:10533000-10534600	Weak transcription	Pancreas	Pancrea
14	chr1:10533000-10534600	Weak transcription	Right Ventricle	heart
15	chr1:10533000-10534600	Weak transcription	Small Intestine	intestine
16	chr1:10533000-10534600	Weak transcription	HSMM	muscle
17	chr1:10533000-10534600	Weak transcription	HUVEC	blood vessel
18	chr1:10533000-10534800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:10533000-10534800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:10533000-10534800	Weak transcription	Esophagus	oesophagus
21	chr1:10533000-10534800	Weak transcription	Gastric	stomach
22	chr1:10533000-10534800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:10533000-10535000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:10533000-10535000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:10533000-10535000	Weak transcription	Aorta	Aorta
26	chr1:10533000-10535000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:10533200-10534600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:10533200-10534600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:10533200-10534600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:10533200-10534600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:10533200-10534600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:10533200-10534600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:10533200-10534600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:10533200-10534600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:10533200-10534600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:10533200-10534600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:10533200-10534600	Enhancers	Primary hematopoietic stem cells	blood
38	chr1:10533200-10534600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:10533200-10534600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:10533200-10534600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:10533200-10534600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:10533200-10534600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:10533200-10534600	Weak transcription	Brain Angular Gyrus	brain
44	chr1:10533200-10534600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:10533200-10534600	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:10533200-10534600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:10533200-10534600	Weak transcription	Colonic Mucosa	Colon
48	chr1:10533200-10534600	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:10533200-10534600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:10533200-10534600	Weak transcription	Fetal Kidney	kidney

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