Variant report

Variant	rs553886431
Chromosome Location	chr3:23959550-23959551
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:121)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:121 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr3:23958136-23959699	HepG2	liver:	n/a	chr3:23958483-23958498
2	POLR2A	chr3:23958105-23960665	K562	blood:	n/a	n/a
3	POLR2A	chr3:23958098-23960725	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:23958121-23960749	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:23958042-23960224	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:23958118-23960215	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:23957960-23959774	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:23959315-23959554	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:23958170-23960433	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:23958032-23960247	GM12891	blood:	n/a	n/a
11	POLR2A	chr3:23958128-23960836	K562	blood:	n/a	n/a
12	CHD1	chr3:23957214-23960192	IMR90	lung:	n/a	n/a
13	POLR2A	chr3:23957643-23960742	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:23957917-23960298	Hela-S3	cervix:	n/a	n/a
15	MYC	chr3:23957965-23959701	K562	blood:	n/a	n/a
16	POLR2A	chr3:23958070-23960273	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:23957917-23960748	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:23958045-23963842	GM12878	blood:	n/a	n/a
19	SIN3A	chr3:23957682-23959805	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZBTB33	chr3:23959248-23959653	K562	blood:	n/a	n/a
21	POLR2A	chr3:23959418-23960170	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr3:23958006-23962277	GM12878	blood:	n/a	n/a
23	WRNIP1	chr3:23958178-23959796	GM12878	blood:	n/a	n/a
24	SREBP1	chr3:23957585-23960048	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:23957976-23965870	K562	blood:	n/a	n/a
26	POLR2A	chr3:23958037-23960741	U87	brain:	n/a	n/a
27	POLR2A	chr3:23958124-23960193	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:23957870-23963941	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr3:23957813-23959917	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:23959431-23959777	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr3:23958124-23959727	ProgFib	skin:	n/a	n/a
32	POLR2A	chr3:23958125-23960796	K562	blood:	n/a	n/a
33	POLR2A	chr3:23958144-23960750	A549	lung:	n/a	n/a
34	POLR2A	chr3:23957955-23959704	GM12878	blood:	n/a	n/a
35	MYC	chr3:23958182-23959582	K562	blood:	n/a	n/a
36	TAF1	chr3:23957862-23959608	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:23958063-23960804	GM12891	blood:	n/a	n/a
38	MAZ	chr3:23957935-23959594	K562	blood:	n/a	n/a
39	CHD1	chr3:23958588-23959934	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:23959433-23959873	K562	blood:	n/a	n/a
41	MYC	chr3:23958101-23959818	K562	blood:	n/a	n/a
42	HEY1	chr3:23958157-23959925	HepG2	liver:	n/a	chr3:23958483-23958498
43	POLR2A	chr3:23957943-23960252	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr3:23957985-23960654	GM18505	blood:	n/a	n/a
45	POLR2A	chr3:23958082-23960833	K562	blood:	n/a	n/a
46	TBL1XR1	chr3:23957940-23960071	K562	blood:	n/a	n/a
47	POU2F2	chr3:23958183-23959624	GM12878	blood:	n/a	chr3:23958462-23958474
48	POLR2A	chr3:23958116-23960115	HL-60	blood:	n/a	n/a
49	POLR2A	chr3:23958086-23959635	A549	lung:	n/a	n/a
50	HA-E2F1	chr3:23957892-23959814	MCF-7	breast:	n/a	chr3:23958468-23958480

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78441071..78441786-chr3:23959166..23959779,2	Hela-S3	cervix:
2	chr3:23846380..23850116-chr3:23956700..23960461,6	MCF-7	breast:
3	chr3:23958569..23960911-chr3:24534140..24537048,3	MCF-7	breast:
4	chr3:23850301..23853237-chr3:23957517..23960615,4	MCF-7	breast:
5	chr3:23742842..23745448-chr3:23959508..23961357,2	K562	blood:
6	chr17:58167241..58170093-chr3:23957521..23960210,2	MCF-7	breast:
7	chr3:23957476..23960072-chr3:25467685..25470119,2	K562	blood:
8	chr3:23958536..23961065-chr3:24535525..24538143,3	K562	blood:
9	chr3:23845393..23848355-chr3:23958587..23960710,4	K562	blood:
10	chr1:203059673..203062550-chr3:23957552..23960185,2	MCF-7	breast:
11	chr3:23852479..23855481-chr3:23956917..23960502,4	MCF-7	breast:
12	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
13	chr3:12873721..12876260-chr3:23958650..23961334,2	K562	blood:
14	chr3:23957534..23959919-chr3:25823926..25825755,2	K562	blood:
15	chr3:23848988..23853074-chr3:23957156..23960234,5	K562	blood:
16	chr3:23845112..23848622-chr3:23958029..23961906,4	K562	blood:
17	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
18	chr3:23957572..23960051-chr3:23995970..23999234,5	MCF-7	breast:

No data

Variant related genes	Relation type
NKIRAS1	TF binding region
ENSG00000151093	Chromatin interaction
ENSG00000272263	Chromatin interaction
ENSG00000166411	Chromatin interaction
ENSG00000151092	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000261040	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000163485	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000077092	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv966996	chr3:23958991-23961257	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23957000-23959600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:23957000-23959600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:23957000-23959600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:23957000-23960400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:23957000-23960600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:23957000-23960600	Active TSS	Right Atrium	heart
7	chr3:23957200-23959600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:23957200-23959600	Active TSS	Stomach Smooth Muscle	stomach
9	chr3:23957200-23959600	Active TSS	HSMMtube	muscle
10	chr3:23957200-23960200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:23957200-23960800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:23957400-23959600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:23957400-23959600	Active TSS	Brain Anterior Caudate	brain
14	chr3:23957400-23959600	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr3:23957400-23959600	Active TSS	Fetal Stomach	stomach
16	chr3:23957400-23959600	Active TSS	Left Ventricle	heart
17	chr3:23957400-23959600	Active TSS	Rectal Smooth Muscle	rectum
18	chr3:23957400-23959600	Active TSS	GM12878-XiMat	blood
19	chr3:23957400-23959600	Active TSS	NHDF-Ad	bronchial
20	chr3:23957400-23959800	Active TSS	Ovary	ovary
21	chr3:23957400-23960800	Active TSS	Psoas Muscle	Psoas
22	chr3:23957400-23960800	Active TSS	Right Ventricle	heart
23	chr3:23957600-23959600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:23957600-23959600	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr3:23957600-23959600	Active TSS	Liver	Liver
26	chr3:23957600-23959600	Active TSS	Brain Hippocampus Middle	brain
27	chr3:23957600-23959600	Active TSS	Fetal Brain Male	brain
28	chr3:23957600-23959600	Active TSS	Fetal Intestine Large	intestine
29	chr3:23957600-23959600	Active TSS	Fetal Muscle Trunk	muscle
30	chr3:23957600-23959600	Active TSS	Placenta	Placenta
31	chr3:23957600-23959600	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:23957600-23959600	Bivalent/Poised TSS	HepG2	liver
33	chr3:23957600-23960200	Active TSS	Fetal Intestine Small	intestine
34	chr3:23957600-23960800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:23957800-23959600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:23957800-23959600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:23957800-23959600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:23957800-23959600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr3:23957800-23959600	Active TSS	Primary T cells from cord blood	blood
40	chr3:23957800-23959600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr3:23957800-23959600	Active TSS	Brain Cingulate Gyrus	brain
42	chr3:23957800-23959600	Active TSS	Duodenum Mucosa	Duodenum
43	chr3:23957800-23959600	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:23957800-23959600	Active TSS	Fetal Kidney	kidney
45	chr3:23957800-23959600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:23957800-23959600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr3:23957800-23959800	Active TSS	Colonic Mucosa	Colon
48	chr3:23957800-23959800	Active TSS	Stomach Mucosa	stomach
49	chr3:23957800-23960000	Active TSS	Aorta	Aorta
50	chr3:23957800-23960000	Active TSS	Fetal Heart	heart

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