Variant report

Variant	rs56074233
Chromosome Location	chr1:220426826-220426827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:220426495-220427138	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:220426617-220426894	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:220426582-220427031	Gliobla	brain:	n/a	n/a
4	POLR2A	chr1:220426756-220426957	A549	lung:	n/a	n/a
5	TAF1	chr1:220426747-220426929	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:220426772-220427073	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:220425773-220427310	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:220426584-220427124	MCF-7	breast:	n/a	n/a
9	POLR2A	chr1:220426506-220427001	Hela-S3	cervix:	n/a	n/a
10	POU2F2	chr1:220426722-220426898	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:220426739-220427350	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:220426735-220426981	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:220426744-220426978	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:220426805-220426835	A549	lung:	n/a	n/a
15	POLR2A	chr1:220426736-220426915	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:220426546-220427151	H1-hESC	embryonic stem cell:	n/a	n/a
17	TAF1	chr1:220426728-220426936	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:220426676-220427024	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:220426593-220427027	GM12892	blood:	n/a	n/a
20	POLR2A	chr1:220426591-220427058	K562	blood:	n/a	n/a
21	POLR2A	chr1:220426808-220426985	HepG2	liver:	n/a	n/a
22	TAF1	chr1:220426743-220426872	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:220426686-220426974	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:220426740-220426919	A549	lung:	n/a	n/a
25	POLR2A	chr1:220426714-220427051	GM12891	blood:	n/a	n/a
26	TAF1	chr1:220426723-220426993	H1-hESC	embryonic stem cell:	n/a	n/a
27	SIN3AK20	chr1:220426767-220426851	HepG2	liver:	n/a	n/a
28	HEY1	chr1:220426727-220426984	K562	blood:	n/a	n/a
29	HEY1	chr1:220426724-220426999	K562	blood:	n/a	n/a
30	POLR2A	chr1:220426657-220427010	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:220426643-220426998	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr1:220425886-220428269	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:220426767-220426887	A549	lung:	n/a	n/a
34	POLR2A	chr1:220426731-220426978	A549	lung:	n/a	n/a
35	HEY1	chr1:220426712-220427004	HepG2	liver:	n/a	n/a
36	TAF1	chr1:220426709-220427007	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr1:220426799-220426851	MCF-7	breast:	n/a	n/a
38	POLR2A	chr1:220426490-220427243	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr1:220426685-220426972	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:220426697-220426977	ProgFib	skin:	n/a	n/a
41	EBF1	chr1:220426669-220426916	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:220426668-220427059	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr1:220426558-220426994	MCF-7	breast:	n/a	n/a
44	POLR2A	chr1:220426764-220426897	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:220426586-220427066	MCF-7	breast:	n/a	n/a
46	POLR2A	chr1:220426750-220426907	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220415502..220418514-chr1:220424873..220426907,3	K562	blood:

No data

Variant related genes	Relation type
MORF4L1P1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10863537	0.84[ASN][1000 genomes]
rs11118508	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402633	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12404532	0.89[EUR][1000 genomes]
rs12404566	0.82[EUR][1000 genomes]
rs12409065	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12411242	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12562531	0.89[ASN][1000 genomes]
rs12568267	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1511695	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17565134	0.83[EUR][1000 genomes]
rs2048477	0.90[EUR][1000 genomes]
rs3814345	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4351641	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57557703	0.82[EUR][1000 genomes]
rs59681037	0.82[EUR][1000 genomes]
rs72749210	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526460	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541290	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7543828	0.90[EUR][1000 genomes]
rs7551804	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs866978	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4643	chr1:220397642-220442231	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv945297	chr1:220426814-220434679	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220393000-220441000	Weak transcription	NHDF-Ad	bronchial
2	chr1:220416000-220442600	Weak transcription	Fetal Heart	heart
3	chr1:220418200-220431400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:220420000-220427000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:220420400-220427000	ZNF genes & repeats	GM12878-XiMat	blood
6	chr1:220420600-220427400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
7	chr1:220421000-220436800	Weak transcription	Fetal Kidney	kidney
8	chr1:220422000-220427000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:220423000-220443400	Weak transcription	Psoas Muscle	Psoas
10	chr1:220423200-220428200	Weak transcription	Stomach Mucosa	stomach
11	chr1:220423400-220427400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:220423400-220443400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:220423400-220443400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:220423600-220427000	Strong transcription	Brain Hippocampus Middle	brain
15	chr1:220423600-220427200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:220423600-220427200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:220423600-220427200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:220423600-220428600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:220423600-220429000	Weak transcription	Brain Angular Gyrus	brain
20	chr1:220423600-220440400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:220423800-220427400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:220423800-220427600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:220423800-220427800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:220423800-220430000	Weak transcription	Fetal Brain Male	brain
25	chr1:220423800-220442600	Weak transcription	Hela-S3	cervix
26	chr1:220424400-220427000	Strong transcription	Fetal Lung	lung
27	chr1:220424400-220439600	Weak transcription	HMEC	breast
28	chr1:220424800-220427000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:220424800-220427000	Strong transcription	Fetal Brain Female	brain
30	chr1:220425000-220427400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:220425200-220427000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:220425200-220427000	ZNF genes & repeats	Fetal Stomach	stomach
33	chr1:220425200-220427000	Strong transcription	Thymus	Thymus
34	chr1:220425200-220427200	Strong transcription	Liver	Liver
35	chr1:220425200-220427400	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:220425200-220427400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:220425200-220431400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:220425200-220443400	Weak transcription	HUVEC	blood vessel
39	chr1:220425400-220427000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:220425400-220427000	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr1:220425400-220427000	Strong transcription	Lung	lung
42	chr1:220425400-220427200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:220425400-220427400	Strong transcription	K562	blood
44	chr1:220425400-220427400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:220425400-220427600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:220425600-220427000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:220425800-220427000	ZNF genes & repeats	Brain Germinal Matrix	brain
48	chr1:220425800-220427000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:220425800-220427400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:220426000-220427000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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