Variant report

Variant	rs562439412
Chromosome Location	chr1:161129905-161129906
allele	A/C
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	chr1:161128767-161130122	PFSK-1	brain:	n/a	n/a
2	MAX	chr1:161128553-161129981	A549	lung:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
3	POLR2A	chr1:161128854-161129916	Raji	blood:	n/a	n/a
4	YY1	chr1:161128765-161129906	H1-hESC	embryonic stem cell:	n/a	chr1:161129194-161129208 chr1:161129303-161129323 chr1:161129309-161129321
5	POLR2A	chr1:161128599-161129918	GM12878	blood:	n/a	n/a
6	MAX	chr1:161128410-161129925	K562	blood:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
7	POLR2A	chr1:161128814-161130166	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:161128826-161129980	H1-neurons	neurons:	n/a	n/a
9	REST	chr1:161128544-161130147	H1-neurons	neurons:	n/a	chr1:161129591-161129604
10	POLR2A	chr1:161128483-161130088	K562	blood:	n/a	n/a
11	YY1	chr1:161128742-161129943	K562	blood:	n/a	chr1:161129194-161129208 chr1:161129303-161129323 chr1:161129309-161129321
12	YY1	chr1:161128697-161129957	H1-hESC	embryonic stem cell:	n/a	chr1:161129194-161129208 chr1:161129303-161129323 chr1:161129309-161129321
13	POLR2A	chr1:161128624-161130284	HepG2	liver:	n/a	n/a
14	RFX5	chr1:161129836-161129928	K562	blood:	n/a	n/a
15	YY1	chr1:161128619-161129916	SK-N-SH	brain:	n/a	chr1:161129194-161129208 chr1:161129303-161129323 chr1:161129309-161129321
16	POLR2A	chr1:161128573-161130479	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:161128536-161129996	HL-60	blood:	n/a	n/a
18	POLR2A	chr1:161128554-161130062	GM12892	blood:	n/a	n/a
19	POLR2A	chr1:161128701-161130357	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:161128568-161130055	K562	blood:	n/a	n/a
21	MAZ	chr1:161128742-161130037	IMR90	lung:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
22	POLR2A	chr1:161128379-161130298	K562	blood:	n/a	n/a
23	HCFC1	chr1:161128410-161130377	Hela-S3	cervix:	n/a	n/a
24	REST	chr1:161128627-161130041	A549	lung:	n/a	chr1:161129591-161129604
25	POLR2A	chr1:161128544-161130028	GM12892	blood:	n/a	n/a
26	POLR2A	chr1:161128335-161130429	K562	blood:	n/a	n/a
27	POLR2A	chr1:161128768-161129942	GM12891	blood:	n/a	n/a
28	POLR2A	chr1:161128659-161129953	H1-hESC	embryonic stem cell:	n/a	n/a
29	HCFC1	chr1:161128897-161129921	K562	blood:	n/a	n/a
30	HEY1	chr1:161129006-161130368	K562	blood:	n/a	n/a
31	POLR2A	chr1:161128795-161129947	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr1:161128550-161131005	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr1:161128754-161130534	HUVEC	blood vessel:	n/a	n/a
34	SIN3A	chr1:161128833-161129987	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:161128188-161130127	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr1:161128688-161129958	H1-hESC	embryonic stem cell:	n/a	n/a
37	YY1	chr1:161128830-161129910	ECC-1	luminal epithelium:	n/a	chr1:161129194-161129208 chr1:161129303-161129323 chr1:161129309-161129321
38	CHD2	chr1:161128971-161130265	K562	blood:	n/a	chr1:161129553-161129560
39	POLR2A	chr1:161128410-161130469	HepG2	liver:	n/a	n/a
40	BCL3	chr1:161128703-161130013	A549	lung:	n/a	chr1:161129563-161129576
41	CHD2	chr1:161129722-161129922	GM12878	blood:	n/a	n/a
42	TAF1	chr1:161128867-161129938	ECC-1	luminal epithelium:	n/a	n/a
43	MXI1	chr1:161128262-161129915	IMR90	lung:	n/a	n/a
44	POLR2A	chr1:161128653-161129991	GM12891	blood:	n/a	n/a
45	POLR2A	chr1:161128344-161130244	A549	lung:	n/a	n/a
46	POLR2A	chr1:161128656-161129936	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr1:161128573-161130103	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr1:161128517-161129913	K562	blood:	n/a	n/a
49	POLR2A	chr1:161128889-161129969	H1-neurons	neurons:	n/a	n/a
50	NR2F2	chr1:161128302-161129928	K562	blood:	n/a	chr1:161129723-161129738

No.	Distal block	Cell Line	Cell type
1	chr1:161100691..161104235-chr1:161128857..161130819,4	K562	blood:
2	chr1:161067905..161072134-chr1:161127935..161131211,3	MCF-7	breast:
3	chr1:160231832..160233674-chr1:161127837..161130606,2	MCF-7	breast:
4	chr1:160989787..160992592-chr1:161127591..161130267,2	K562	blood:
5	chr1:161101050..161105947-chr1:161126092..161130683,11	K562	blood:
6	chr1:161128751..161130724-chr1:161170850..161173844,2	MCF-7	breast:
7	chr1:161129146..161131988-chr1:161170465..161172275,2	MCF-7	breast:
8	chr1:161085978..161089990-chr1:161127865..161134037,11	K562	blood:
9	chr1:161052998..161054950-chr1:161128036..161130636,2	MCF-7	breast:
10	chr1:161011414..161013032-chr1:161129851..161132212,2	K562	blood:
11	chr1:160989693..160991522-chr1:161127596..161130418,2	MCF-7	breast:
12	chr1:161101282..161104235-chr1:161127986..161130833,4	MCF-7	breast:
13	chr1:161085658..161090812-chr1:161125926..161133105,17	K562	blood:
14	chr1:161128018..161129911-chr1:161170467..161173789,3	K562	blood:

Variant related genes	Relation type
USP21	TF binding region
ENSG00000224985	TF binding region
ENSG00000162755	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000132716	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000158864	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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv3489555	chr1:161129735-161131477	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	n/a
3	esv3489556	chr1:161129735-161131477	Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 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	chr1:161128600-161130000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr1:161128600-161130000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:161128600-161130000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:161128600-161130200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:161128600-161130800	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr1:161128800-161130000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:161128800-161130000	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:161128800-161130000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:161128800-161130000	Active TSS	Psoas Muscle	Psoas
10	chr1:161128800-161130200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:161129000-161130000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:161129000-161130000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:161129000-161130000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:161129000-161130000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:161129000-161130000	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr1:161129000-161130000	Active TSS	Colon Smooth Muscle	Colon
17	chr1:161129000-161130000	Active TSS	Fetal Kidney	kidney
18	chr1:161129000-161130000	Active TSS	Left Ventricle	heart
19	chr1:161129000-161130000	Active TSS	Small Intestine	intestine
20	chr1:161129000-161130000	Active TSS	A549	lung
21	chr1:161129000-161130200	Active TSS	Brain Angular Gyrus	brain
22	chr1:161129000-161130200	Active TSS	Right Atrium	heart
23	chr1:161129000-161130400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr1:161129000-161130400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr1:161129200-161130000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:161129200-161130000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:161129600-161130000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:161129600-161130000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr1:161129600-161130000	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr1:161129600-161130000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr1:161129600-161130000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:161129600-161130000	Flanking Active TSS	Placenta	Placenta
33	chr1:161129600-161130200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr1:161129600-161130200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr1:161129600-161130200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:161129600-161130200	Flanking Active TSS	Liver	Liver
37	chr1:161129600-161130200	Flanking Active TSS	Fetal Thymus	thymus
38	chr1:161129600-161130200	Flanking Active TSS	Stomach Mucosa	stomach
39	chr1:161129600-161130200	Flanking Active TSS	HUVEC	blood vessel
40	chr1:161129600-161130400	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr1:161129600-161130400	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr1:161129600-161130400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:161129600-161130400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:161129600-161130400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:161129600-161130400	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr1:161129600-161130400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:161129600-161130400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr1:161129600-161130400	Flanking Active TSS	Thymus	Thymus
49	chr1:161129600-161130600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr1:161129600-161130600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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