Variant report

Variant	rs557420639
Chromosome Location	chr1:225615051-225615052
allele	C/T
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	JUN	chr1:225611820-225617257	K562	blood:	n/a	chr1:225613227-225613237 chr1:225616567-225616575 chr1:225615250-225615261 chr1:225616568-225616575 chr1:225612971-225612983 chr1:225616565-225616577 chr1:225613226-225613238 chr1:225613227-225613237 chr1:225613228-225613236 chr1:225616567-225616575 chr1:225615989-225615998 chr1:225612930-225612939 chr1:225613227-225613237 chr1:225616648-225616657 chr1:225615862-225615871 chr1:225616566-225616576
2	MAX	chr1:225613853-225616765	NB4	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
3	ZBTB7A	chr1:225614737-225615822	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:225614632-225616632	NB4	blood:	n/a	n/a
5	SIN3AK20	chr1:225614444-225615281	A549	lung:	n/a	n/a
6	POLR2A	chr1:225613990-225616782	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:225615028-225615324	GM12878	blood:	n/a	n/a
8	SIN3AK20	chr1:225614576-225616599	SK-N-SH	brain:	n/a	n/a
9	MYC	chr1:225614532-225615187	MCF10A-Er-Src	breast:	n/a	chr1:225614720-225614727 chr1:225614718-225614728
10	ZKSCAN1	chr1:225614308-225615218	Hela-S3	cervix:	n/a	n/a
11	HA-E2F1	chr1:225614602-225616606	MCF-7	breast:	n/a	chr1:225615950-225615962 chr1:225615904-225615913 chr1:225615329-225615339 chr1:225615352-225615361 chr1:225615306-225615313 chr1:225615443-225615453 chr1:225616360-225616372 chr1:225615950-225615959 chr1:225615442-225615451 chr1:225615446-225615456 chr1:225614769-225614779 chr1:225615326-225615336 chr1:225616358-225616368
12	POLR2A	chr1:225611871-225615203	K562	blood:	n/a	n/a
13	HDAC2	chr1:225614611-225615151	HepG2	liver:	n/a	n/a
14	MAX	chr1:225614514-225615507	K562	blood:	n/a	chr1:225614720-225614727 chr1:225614718-225614728
15	POLR2A	chr1:225614360-225616711	GM19193	blood:	n/a	n/a
16	POLR2A	chr1:225614318-225616602	K562	blood:	n/a	n/a
17	RFX5	chr1:225614209-225615399	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr1:225613968-225616747	IMR90	lung:	n/a	n/a
19	YY1	chr1:225615031-225616543	HepG2	liver:	n/a	chr1:225615439-225615450 chr1:225615950-225615959 chr1:225615442-225615451 chr1:225615350-225615372 chr1:225615445-225615454 chr1:225615352-225615361
20	POLR2A	chr1:225614388-225616860	GM18951	blood:	n/a	n/a
21	CHD1	chr1:225614071-225616836	IMR90	lung:	n/a	chr1:225615951-225615961 chr1:225615306-225615313 chr1:225615930-225615940
22	CCNT2	chr1:225614391-225616764	K562	blood:	n/a	chr1:225615950-225615959 chr1:225616020-225616040
23	PAX5	chr1:225615029-225615411	GM12892	blood:	n/a	n/a
24	MXI1	chr1:225614587-225616584	HepG2	liver:	n/a	n/a
25	MAX	chr1:225614301-225616741	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
26	RCOR1	chr1:225614212-225615063	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr1:225615000-225615150	AoAF	blood vessel:	n/a	n/a
28	E2F6	chr1:225614574-225615410	H1-hESC	embryonic stem cell:	n/a	chr1:225615329-225615339 chr1:225615352-225615361 chr1:225615306-225615313 chr1:225614769-225614779 chr1:225615326-225615336
29	HDAC2	chr1:225614563-225615559	MCF-7	breast:	n/a	n/a
30	REST	chr1:225614090-225616919	H1-neurons	neurons:	n/a	chr1:225614567-225614585 chr1:225615143-225615163 chr1:225615628-225615641 chr1:225615409-225615422 chr1:225615612-225615625 chr1:225614778-225614791 chr1:225615226-225615240 chr1:225615617-225615627
31	POLR2A	chr1:225614401-225615181	K562	blood:	n/a	n/a
32	HMGN3	chr1:225614620-225616660	K562	blood:	n/a	n/a
33	TCF7L2	chr1:225614236-225615558	Hela-S3	cervix:	n/a	n/a
34	HA-E2F1	chr1:225614359-225616524	Hela-S3	cervix:	n/a	chr1:225615950-225615962 chr1:225615904-225615913 chr1:225615329-225615339 chr1:225615352-225615361 chr1:225615306-225615313 chr1:225615443-225615453 chr1:225616360-225616372 chr1:225615950-225615959 chr1:225615442-225615451 chr1:225615446-225615456 chr1:225614769-225614779 chr1:225615326-225615336 chr1:225616358-225616368
35	POLR2A	chr1:225614671-225616720	K562	blood:	n/a	n/a
36	MAX	chr1:225614597-225615374	A549	lung:	n/a	chr1:225614720-225614727 chr1:225614718-225614728
37	TBL1XR1	chr1:225614574-225615139	K562	blood:	n/a	n/a
38	MXI1	chr1:225614100-225616612	Hela-S3	cervix:	n/a	n/a
39	SIN3A	chr1:225614170-225616776	H1-hESC	embryonic stem cell:	n/a	chr1:225615322-225615333
40	MAX	chr1:225614424-225616863	ECC-1	luminal epithelium:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
41	POLR2A	chr1:225614985-225616600	GM12878	blood:	n/a	n/a
42	ETS1	chr1:225614514-225615405	K562	blood:	n/a	n/a
43	SIN3AK20	chr1:225614867-225616600	PANC-1	pancreas:	n/a	n/a
44	MTA3	chr1:225614339-225615379	GM12878	blood:	n/a	n/a
45	TCF12	chr1:225615021-225616671	ECC-1	luminal epithelium:	n/a	chr1:225615592-225615602
46	TEAD4	chr1:225613826-225615416	K562	blood:	n/a	chr1:225614248-225614257
47	PAX5	chr1:225614990-225615261	GM12878	blood:	n/a	n/a
48	NFIC	chr1:225614854-225615127	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:225613030-225616753	K562	blood:	n/a	n/a
50	E2F6	chr1:225614485-225615290	A549	lung:	n/a	chr1:225614769-225614779

No.	Distal block	Cell Line	Cell type
1	chr1:225605937..225609657-chr1:225612868..225616965,5	MCF-7	breast:
2	chr1:225590339..225593004-chr1:225614495..225616348,2	MCF-7	breast:
3	chr1:225614646..225616665-chr1:226249352..226251446,2	K562	blood:
4	chr1:225607872..225610815-chr1:225614150..225617627,4	MCF-7	breast:
5	chr1:225609832..225612207-chr1:225614120..225615659,2	MCF-7	breast:
6	chr1:225604992..225607166-chr1:225612913..225616218,4	MCF-7	breast:
7	chr1:225569904..225572339-chr1:225612601..225615493,2	K562	blood:

Variant related genes	Relation type
LBR	TF binding region
ENSG00000272562	Chromatin interaction
ENSG00000143815	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv3342670	chr1:225614754-225617302	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225609600-225615200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:225612000-225615400	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr1:225612400-225615200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:225612600-225615200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr1:225612600-225615200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:225613800-225615200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:225613800-225615200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr1:225613800-225615200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr1:225613800-225616600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:225613800-225616600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:225613800-225616800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr1:225614000-225615200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:225614000-225615200	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr1:225614000-225615200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr1:225614000-225616600	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:225614000-225616600	Active TSS	A549	lung
17	chr1:225614000-225616800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:225614000-225616800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:225614000-225616800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:225614000-225616800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:225614000-225616800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:225614000-225616800	Active TSS	Fetal Kidney	kidney
23	chr1:225614000-225616800	Active TSS	Right Ventricle	heart
24	chr1:225614000-225616800	Active TSS	Thymus	Thymus
25	chr1:225614000-225616800	Active TSS	NHDF-Ad	bronchial
26	chr1:225614000-225617000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:225614000-225617000	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:225614000-225617000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr1:225614200-225615200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:225614200-225615200	Flanking Active TSS	Left Ventricle	heart
31	chr1:225614200-225616600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:225614200-225616600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:225614200-225616600	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr1:225614200-225616600	Active TSS	Gastric	stomach
35	chr1:225614200-225616600	Active TSS	Ovary	ovary
36	chr1:225614200-225616600	Active TSS	Small Intestine	intestine
37	chr1:225614200-225616800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:225614200-225616800	Active TSS	GM12878-XiMat	blood
39	chr1:225614200-225617200	Active TSS	NHLF	lung
40	chr1:225614400-225615200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr1:225614400-225615200	Active TSS	Fetal Heart	heart
42	chr1:225614400-225615200	Flanking Active TSS	Placenta	Placenta
43	chr1:225614400-225616400	Bivalent/Poised TSS	HepG2	liver
44	chr1:225614400-225616600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:225614400-225616600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:225614400-225616600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:225614400-225616600	Active TSS	Lung	lung
48	chr1:225614400-225616600	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr1:225614400-225616600	Active TSS	Hela-S3	cervix
50	chr1:225614400-225616800	Active TSS	Aorta	Aorta

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