Variant report

Variant	rs2355365
Chromosome Location	chr1:45109101-45109102
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	chr1:45106886-45109812	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:45108404-45109228	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:45107134-45111325	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:45107311-45109797	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:45107417-45109443	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:45108862-45109280	K562	blood:	n/a	n/a
7	POLR2A	chr1:45107334-45109174	GM12891	blood:	n/a	n/a
8	POLR2A	chr1:45107469-45109768	A549	lung:	n/a	n/a
9	POLR2A	chr1:45108938-45109194	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:45107006-45109811	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:45106850-45111423	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:45107298-45109279	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45105542..45109261-chr1:45139821..45142236,3	K562	blood:
2	chr1:45107794..45110562-chr1:45112679..45115403,3	MCF-7	breast:

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

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1051648	0.90[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs11581172	0.90[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs11582970	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588956	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs12728857	0.85[JPT][hapmap]
rs12731688	0.93[EUR][1000 genomes]
rs1407144	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs17387413	0.90[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs2018706	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs2236219	0.82[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs2281759	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2822	0.90[CEU][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs34296911	0.95[EUR][1000 genomes]
rs3444	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35791258	0.92[EUR][1000 genomes]
rs3754421	0.85[ASN][1000 genomes]
rs3768439	0.95[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3768441	0.85[ASN][1000 genomes]
rs3850852	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs41269061	0.94[EUR][1000 genomes]
rs4660283	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs4660284	0.95[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660285	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660814	0.85[ASN][1000 genomes]
rs4660815	0.95[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs4660816	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs4660817	0.94[EUR][1000 genomes]
rs56756630	0.85[ASN][1000 genomes]
rs57291201	0.93[EUR][1000 genomes]
rs59834392	0.85[ASN][1000 genomes]
rs72671943	0.85[ASN][1000 genomes]
rs72671948	0.85[ASN][1000 genomes]
rs72671949	0.85[ASN][1000 genomes]
rs72671954	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74070566	0.86[EUR][1000 genomes]
rs876511	0.95[EUR][1000 genomes]
rs876512	0.95[EUR][1000 genomes]
rs995089	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[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	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	chr1:45099000-45111400	Genic enhancers	Colon Smooth Muscle	Colon
3	chr1:45099000-45115600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:45099000-45116800	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr1:45099000-45117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:45099000-45117800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:45099200-45109200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:45099200-45111400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:45099200-45117600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:45099200-45118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:45099400-45110600	Strong transcription	Osteobl	bone
12	chr1:45099400-45115000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:45099400-45115600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:45099400-45117200	Strong transcription	Placenta	Placenta
15	chr1:45099400-45120800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:45099400-45121000	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:45099400-45121200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:45099600-45110200	Strong transcription	NHLF	lung
19	chr1:45099600-45110400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:45099600-45114600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:45099600-45115400	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr1:45099600-45115600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:45099600-45117200	Strong transcription	Primary B cells from cord blood	blood
24	chr1:45099600-45117200	Strong transcription	Primary hematopoietic stem cells	blood
25	chr1:45099600-45118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:45099600-45118800	Strong transcription	Fetal Thymus	thymus
27	chr1:45099800-45110600	Strong transcription	Colonic Mucosa	Colon
28	chr1:45099800-45115400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:45099800-45117400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:45099800-45118200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:45099800-45118400	Strong transcription	Thymus	Thymus
32	chr1:45099800-45121200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:45099800-45121600	Strong transcription	Brain Germinal Matrix	brain
34	chr1:45099800-45125600	Strong transcription	Lung	lung
35	chr1:45100000-45113600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:45100000-45113600	Strong transcription	Hela-S3	cervix
37	chr1:45100000-45117400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:45100000-45118600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:45100200-45111000	Strong transcription	Fetal Intestine Large	intestine
40	chr1:45100200-45117400	Strong transcription	HepG2	liver
41	chr1:45100200-45118000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr1:45100200-45119800	Strong transcription	Primary T cells from cord blood	blood
43	chr1:45100400-45109600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:45100400-45111800	Strong transcription	Fetal Intestine Small	intestine
45	chr1:45100400-45114600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:45100400-45117200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:45100400-45117400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:45100400-45118400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:45100400-45120800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:45100600-45117200	Strong transcription	Dnd41	blood

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