Variant report

Variant	rs4660815
Chromosome Location	chr1:45100098-45100099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45099647-45100488	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:45098876-45100499	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:45096631-45100261	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45096207-45100173	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:45098980-45100198	K562	blood:	n/a	n/a
6	POLR2A	chr1:45100077-45100148	K562	blood:	n/a	n/a
7	POLR2A	chr1:45099152-45100105	GM12891	blood:	n/a	n/a
8	POLR2A	chr1:45099402-45100838	K562	blood:	n/a	n/a
9	POLR2A	chr1:45096570-45100273	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:45100045-45100914	K562	blood:	n/a	n/a
11	POLR2A	chr1:45098539-45100201	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:45100095-45100114	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:45098947-45100691	GM12892	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45077147..45081258-chr1:45096476..45100107,4	MCF-7	breast:
2	chr1:45096334..45100885-chr1:45195106..45197628,6	K562	blood:
3	chr1:45097570..45100220-chr1:45105727..45109004,3	MCF-7	breast:
4	chr1:45095169..45100377-chr1:45133934..45142864,15	K562	blood:
5	chr1:45091834..45094647-chr1:45100049..45102686,2	MCF-7	breast:
6	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:
7	chr1:45096002..45100159-chr1:45110119..45116077,6	MCF-7	breast:

No data

Variant related genes	Relation type
RNF220	TF binding region
ENSG00000199377	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000126106	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000187147	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1051648	0.95[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1051664	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs11581172	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17387413	0.95[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17880829	1.00[CHB][hapmap]
rs17884316	1.00[CHB][hapmap]
rs17884653	1.00[CHB][hapmap]
rs2018706	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281759	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs2355365	0.95[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs2822	0.95[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34296911	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3444	0.90[CEU][hapmap];0.87[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs35791258	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768439	0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[MKK][hapmap];0.90[TSI][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	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4660283	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660284	0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs4660285	0.93[EUR][1000 genomes]
rs4660816	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	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57291201	0.92[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs995089	0.95[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][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	chr1:45098400-45101200	Weak transcription	Small Intestine	intestine
2	chr1:45098400-45101400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:45098400-45101400	Weak transcription	Ovary	ovary
4	chr1:45098400-45103400	Genic enhancers	Esophagus	oesophagus
5	chr1:45098400-45116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:45098600-45100200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:45098600-45100400	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr1:45098600-45100400	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr1:45098600-45100600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:45098600-45100600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:45098600-45100800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:45098600-45101000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:45098600-45101400	Genic enhancers	Brain Cingulate Gyrus	brain
14	chr1:45098600-45102000	Genic enhancers	Brain Inferior Temporal Lobe	brain
15	chr1:45098800-45100200	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:45098800-45100200	Enhancers	Fetal Heart	heart
17	chr1:45098800-45100200	Genic enhancers	Fetal Intestine Large	intestine
18	chr1:45098800-45100400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:45098800-45100400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:45098800-45100400	Genic enhancers	Fetal Intestine Small	intestine
21	chr1:45098800-45100400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr1:45098800-45100400	Genic enhancers	Fetal Muscle Leg	muscle
23	chr1:45098800-45100600	Enhancers	Right Atrium	heart
24	chr1:45098800-45101000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:45098800-45101200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:45098800-45101200	Weak transcription	Fetal Brain Male	brain
27	chr1:45098800-45101800	Genic enhancers	Brain Hippocampus Middle	brain
28	chr1:45098800-45103800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:45099000-45100200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:45099000-45100200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:45099000-45100200	Genic enhancers	HepG2	liver
32	chr1:45099000-45100400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:45099000-45100400	Genic enhancers	Adipose Nuclei	Adipose
34	chr1:45099000-45100400	Genic enhancers	Duodenum Mucosa	Duodenum
35	chr1:45099000-45100400	Genic enhancers	Monocytes-CD14+_RO01746	blood
36	chr1:45099000-45100800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:45099000-45101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:45099000-45101000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:45099000-45101000	Strong transcription	Fetal Kidney	kidney
40	chr1:45099000-45101600	Genic enhancers	Brain Angular Gyrus	brain
41	chr1:45099000-45101600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:45099000-45102000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:45099000-45102000	Genic enhancers	Brain Substantia Nigra	brain
44	chr1:45099000-45102000	Strong transcription	HSMMtube	muscle
45	chr1:45099000-45102200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:45099000-45103600	Genic enhancers	Fetal Brain Female	brain
47	chr1:45099000-45103800	Genic enhancers	Spleen	Spleen
48	chr1:45099000-45104200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:45099000-45108600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr1:45099000-45111400	Genic enhancers	Colon Smooth Muscle	Colon

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