Variant report

Variant	rs11580599
Chromosome Location	chr1:228335959-228335960
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	chr1:228332644-228338827	K562	blood:	n/a	n/a
2	POLR2A	chr1:228335762-228339602	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228335884-228339752	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:228335864-228336179	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228295623..228298108-chr1:228335544..228338438,2	MCF-7	breast:
2	chr1:228289424..228292369-chr1:228333748..228336393,2	MCF-7	breast:
3	chr1:228267816..228271023-chr1:228334433..228337364,3	K562	blood:

Variant related genes	Relation type
GJC2	TF binding region
ENSG00000162910	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000143793	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10127705	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495278	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916266	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1094602	0.96[EUR][1000 genomes]
rs1094603	0.96[EUR][1000 genomes]
rs11577976	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11581169	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11582265	0.83[AFR][1000 genomes]
rs11582369	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11586055	0.80[EUR][1000 genomes]
rs12034268	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12039801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12048010	0.83[AFR][1000 genomes]
rs1771486	0.88[EUR][1000 genomes]
rs1803695	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28587961	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34687764	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3768330	0.83[AFR][1000 genomes]
rs3795773	0.96[EUR][1000 genomes]
rs3795774	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41303083	0.96[EUR][1000 genomes]
rs4653906	0.86[EUR][1000 genomes]
rs4653908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653909	0.86[EUR][1000 genomes]
rs4653914	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57146523	0.83[AFR][1000 genomes]
rs57657087	0.83[AFR][1000 genomes]
rs61501937	0.80[EUR][1000 genomes]
rs61825156	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825157	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61825159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6663726	0.86[EUR][1000 genomes]
rs6668719	0.86[EUR][1000 genomes]
rs7530253	0.96[EUR][1000 genomes]
rs7537552	0.86[EUR][1000 genomes]
rs882451	0.83[AFR][1000 genomes]
rs9287011	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9970544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
8	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
9	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
10	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
11	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv549290	chr1:228333652-228349806	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv873258	chr1:228334088-228359775	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
15	nsv873259	chr1:228334277-228359775	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
16	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228329000-228336800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:228329000-228339400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:228329000-228339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:228329200-228337400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:228329400-228336600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:228329400-228337600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:228329400-228337600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:228329400-228338200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:228329600-228336800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:228329800-228336400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:228329800-228336600	Weak transcription	A549	lung
12	chr1:228330000-228337200	Genic enhancers	Fetal Muscle Leg	muscle
13	chr1:228330000-228337800	Genic enhancers	Lung	lung
14	chr1:228330200-228336200	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:228330600-228337200	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr1:228331000-228338800	Weak transcription	HSMMtube	muscle
17	chr1:228331200-228336000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:228331400-228341800	Weak transcription	Psoas Muscle	Psoas
19	chr1:228331600-228337000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:228331600-228337000	Weak transcription	NH-A	brain
21	chr1:228331600-228341000	Genic enhancers	Fetal Thymus	thymus
22	chr1:228331800-228336400	Weak transcription	NHDF-Ad	bronchial
23	chr1:228331800-228336600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:228331800-228336800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:228332000-228336200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:228332000-228336400	Weak transcription	Hela-S3	cervix
27	chr1:228332000-228336400	Weak transcription	HSMM	muscle
28	chr1:228332000-228336600	Weak transcription	Fetal Heart	heart
29	chr1:228332000-228337000	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr1:228332200-228336000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:228332200-228336200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:228332200-228337400	Strong transcription	Dnd41	blood
33	chr1:228332400-228336400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:228332400-228337200	Genic enhancers	Esophagus	oesophagus
35	chr1:228332400-228339400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:228332600-228336200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr1:228332600-228336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:228332600-228337600	Weak transcription	Small Intestine	intestine
39	chr1:228332600-228338200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:228332800-228337800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:228332800-228338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:228332800-228339000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:228332800-228349800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:228333000-228336200	Strong transcription	Brain Anterior Caudate	brain
45	chr1:228333000-228336600	Strong transcription	Colonic Mucosa	Colon
46	chr1:228333000-228336600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:228333000-228336800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:228333000-228336800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:228333000-228337000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr1:228333000-228337200	Strong transcription	Liver	Liver

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