Variant report

Variant	rs56355022
Chromosome Location	chr2:20442989-20442990
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	chr2:20442332-20444596	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:20442403-20443308	U87	brain:	n/a	n/a
3	POLR2A	chr2:20442389-20443788	GM12891	blood:	n/a	n/a
4	POLR2A	chr2:20442951-20443107	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:20442372-20443129	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr2:20442359-20444693	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:20442349-20447377	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr2:20442967-20443218	U87	brain:	n/a	n/a
9	POLR2A	chr2:20442912-20443262	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:20442473-20443224	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr2:20442523-20443374	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:20442917-20443227	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr2:20442384-20443265	GM12891	blood:	n/a	n/a
14	GTF2F1	chr2:20442873-20443035	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:20442319-20444736	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:20442947-20443223	GM12891	blood:	n/a	n/a
17	SRF	chr2:20442683-20443140	H1-hESC	embryonic stem cell:	n/a	chr2:20442940-20442957 chr2:20442939-20442952 chr2:20442940-20442954 chr2:20442938-20442953 chr2:20442937-20442955 chr2:20442940-20442951 chr2:20442941-20442955 chr2:20442937-20442951
18	MAX	chr2:20442704-20443074	H1-hESC	embryonic stem cell:	n/a	chr2:20442737-20442747 chr2:20442865-20442876
19	POLR2A	chr2:20441943-20449974	K562	blood:	n/a	n/a
20	BCL3	chr2:20442965-20443305	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:20442436-20443302	U87	brain:	n/a	n/a
22	POLR2A	chr2:20442856-20443305	GM12892	blood:	n/a	n/a
23	SRF	chr2:20442749-20443029	H1-hESC	embryonic stem cell:	n/a	chr2:20442940-20442957 chr2:20442939-20442952 chr2:20442940-20442954 chr2:20442938-20442953 chr2:20442937-20442955 chr2:20442940-20442951 chr2:20442941-20442955 chr2:20442937-20442951
24	BCL3	chr2:20442520-20443386	A549	lung:	n/a	n/a
25	POLR2A	chr2:20442748-20443146	K562	blood:	n/a	n/a
26	POLR2A	chr2:20442591-20443057	K562	blood:	n/a	n/a
27	POLR2A	chr2:20442608-20443173	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr2:20442795-20443141	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr2:20442459-20447911	GM12878	blood:	n/a	n/a
30	MAX	chr2:20442497-20443087	H1-hESC	embryonic stem cell:	n/a	chr2:20442737-20442747 chr2:20442576-20442587 chr2:20442865-20442876
31	POLR2A	chr2:20442389-20443314	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr2:20442912-20443235	GM12892	blood:	n/a	n/a
33	TBP	chr2:20442961-20443101	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:20442370-20443345	GM12892	blood:	n/a	n/a
35	POLR2A	chr2:20441272-20443298	HepG2	liver:	n/a	n/a
36	E2F6	chr2:20442566-20443210	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr2:20442828-20443287	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr2:20441793-20444944	A549	lung:	n/a	n/a
39	POLR2A	chr2:20442596-20443170	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:20442931-20443313	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr2:20442448-20443267	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:20442378-20446131	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr2:20442799-20443137	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:20442391-20443227	K562	blood:	n/a	n/a
45	POLR2A	chr2:20442962-20443196	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:20442677-20443170	MCF-7	breast:	n/a	n/a
47	POLR2A	chr2:20442429-20443170	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20442462..20444292-chr2:20444678..20446517,2	MCF-7	breast:
2	chr2:20438741..20440683-chr2:20441500..20444456,2	MCF-7	breast:
3	chr2:20437602..20439619-chr2:20440851..20444211,3	MCF-7	breast:
4	chr2:20441679..20444514-chr2:20449489..20452544,3	K562	blood:
5	chr2:20432388..20434846-chr2:20442190..20444125,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235411	TF binding region
ENSG00000238735	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs72787404	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72788909	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1819683	chr2:20423264-20455467	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3449290	chr2:20441521-20443469	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv3438551	chr2:20442021-20443019	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20426000-20447000	Weak transcription	GM12878-XiMat	blood
2	chr2:20431400-20446800	Weak transcription	Spleen	Spleen
3	chr2:20431800-20444200	Weak transcription	A549	lung
4	chr2:20431800-20446200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:20433000-20450200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:20433000-20451200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:20436200-20446600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:20436200-20447000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:20436600-20452600	Weak transcription	Gastric	stomach
10	chr2:20436800-20445800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:20437000-20446400	Weak transcription	Hela-S3	cervix
12	chr2:20437000-20447000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:20437000-20453000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:20437800-20448000	Weak transcription	HMEC	breast
15	chr2:20438000-20445600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:20439400-20447200	Weak transcription	Primary B cells from cord blood	blood
17	chr2:20439800-20450200	Weak transcription	Brain Substantia Nigra	brain
18	chr2:20440200-20444400	Enhancers	Placenta	Placenta
19	chr2:20440600-20443000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:20440600-20446600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:20440600-20447000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:20440600-20451000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:20440600-20452600	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:20440800-20445600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:20440800-20452200	Weak transcription	Brain Angular Gyrus	brain
26	chr2:20440800-20452600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:20441400-20453000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:20441800-20443200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:20441800-20447000	Weak transcription	Adipose Nuclei	Adipose
30	chr2:20441800-20447000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:20442000-20444200	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:20442000-20445600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:20442000-20446000	Weak transcription	Brain Germinal Matrix	brain
34	chr2:20442000-20446200	Weak transcription	Liver	Liver
35	chr2:20442000-20446200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:20442000-20446400	Weak transcription	NHDF-Ad	bronchial
37	chr2:20442000-20446400	Weak transcription	NHLF	lung
38	chr2:20442000-20446800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:20442000-20446800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:20442000-20446800	Weak transcription	Lung	lung
41	chr2:20442000-20447000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:20442000-20447000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:20442000-20447000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:20442000-20447000	Weak transcription	HUVEC	blood vessel
45	chr2:20442000-20447800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:20442000-20448800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:20442000-20449600	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:20442000-20450200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:20442000-20450400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr2:20442000-20450600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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