Variant report

Variant	rs4660816
Chromosome Location	chr1:45104978-45104979
allele	A/G
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	chr1:45104876-45105379	K562	blood:	n/a	n/a
2	POLR2A	chr1:45104827-45105271	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:45104624-45105361	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:45104729-45105553	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:45104605-45105494	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:45104665-45105459	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:45104749-45105359	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45100500..45107773-chr1:45184365..45188884,11	K562	blood:
2	chr1:45090049..45092827-chr1:45102981..45105305,3	MCF-7	breast:
3	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:
4	chr1:45094739..45096419-chr1:45104859..45106473,2	MCF-7	breast:

Variant related genes	Relation type
RNF220	TF binding region
ENSG00000187147	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000198520	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1051648	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1051664	0.80[EUR][1000 genomes]
rs11581172	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11582970	0.90[EUR][1000 genomes]
rs12731688	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1407144	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17387413	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2018706	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281759	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2355365	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs2822	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34296911	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3444	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs35791258	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768439	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs3850852	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41269061	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4660283	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660284	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs4660285	0.93[EUR][1000 genomes]
rs4660815	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660817	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57291201	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72671954	0.95[EUR][1000 genomes]
rs74070566	0.91[EUR][1000 genomes]
rs876511	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs876512	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs995089	0.95[CEU][hapmap];0.95[EUR][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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45098400-45116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45099000-45108600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
3	chr1:45099000-45111400	Genic enhancers	Colon Smooth Muscle	Colon
4	chr1:45099000-45115600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:45099000-45116800	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr1:45099000-45117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:45099000-45117800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:45099200-45105400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:45099200-45108600	Strong transcription	Aorta	Aorta
10	chr1:45099200-45109200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:45099200-45111400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:45099200-45117600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:45099200-45118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:45099400-45106800	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr1:45099400-45107000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:45099400-45108200	Strong transcription	A549	lung
17	chr1:45099400-45110600	Strong transcription	Osteobl	bone
18	chr1:45099400-45115000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:45099400-45115600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:45099400-45117200	Strong transcription	Placenta	Placenta
21	chr1:45099400-45120800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:45099400-45121000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:45099400-45121200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:45099600-45110200	Strong transcription	NHLF	lung
25	chr1:45099600-45110400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:45099600-45114600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:45099600-45115400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr1:45099600-45115600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:45099600-45117200	Strong transcription	Primary B cells from cord blood	blood
30	chr1:45099600-45117200	Strong transcription	Primary hematopoietic stem cells	blood
31	chr1:45099600-45118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:45099600-45118800	Strong transcription	Fetal Thymus	thymus
33	chr1:45099800-45110600	Strong transcription	Colonic Mucosa	Colon
34	chr1:45099800-45115400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:45099800-45117400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:45099800-45118200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:45099800-45118400	Strong transcription	Thymus	Thymus
38	chr1:45099800-45121200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:45099800-45121600	Strong transcription	Brain Germinal Matrix	brain
40	chr1:45099800-45125600	Strong transcription	Lung	lung
41	chr1:45100000-45113600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr1:45100000-45113600	Strong transcription	Hela-S3	cervix
43	chr1:45100000-45117400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:45100000-45118600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:45100200-45105200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:45100200-45107200	Strong transcription	Liver	Liver
47	chr1:45100200-45107600	Strong transcription	Pancreas	Pancrea
48	chr1:45100200-45111000	Strong transcription	Fetal Intestine Large	intestine
49	chr1:45100200-45117400	Strong transcription	HepG2	liver
50	chr1:45100200-45118000	Strong transcription	Primary monocytes fromperipheralblood	blood

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