Variant report

Variant	rs538538293
Chromosome Location	chr3:138666548-138666549
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	ZBTB7A	chr3:138665318-138666608	K562	blood:	n/a	n/a
2	ZMIZ1	chr3:138666445-138666680	K562	blood:	n/a	n/a
3	TBL1XR1	chr3:138666427-138666933	K562	blood:	n/a	n/a
4	SMARCB1	chr3:138664989-138666842	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr3:138665017-138666795	K562	blood:	n/a	chr3:138666114-138666124
6	MAFK	chr3:138666404-138666895	K562	blood:	n/a	n/a
7	CTCF	chr3:138666211-138666690	K562	blood:	n/a	n/a
8	TAF1	chr3:138664973-138666613	K562	blood:	n/a	n/a
9	POLR2A	chr3:138664890-138666825	K562	blood:	n/a	n/a
10	SIN3A	chr3:138665532-138666575	H1-hESC	embryonic stem cell:	n/a	chr3:138665612-138665625 chr3:138666039-138666050 chr3:138665609-138665618
11	HEY1	chr3:138665462-138666614	K562	blood:	n/a	chr3:138665812-138665827
12	TBP	chr3:138664919-138666740	K562	blood:	n/a	n/a
13	MAX	chr3:138663821-138666675	K562	blood:	n/a	chr3:138666114-138666124
14	E2F6	chr3:138663661-138666655	H1-hESC	embryonic stem cell:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
15	RCOR1	chr3:138665037-138666727	K562	blood:	n/a	n/a
16	UBTF	chr3:138664715-138666727	K562	blood:	n/a	n/a
17	POLR2A	chr3:138665608-138666744	Hela-S3	cervix:	n/a	n/a
18	MYC	chr3:138665617-138666775	K562	blood:	n/a	chr3:138666114-138666124
19	POLR2A	chr3:138664719-138666765	K562	blood:	n/a	n/a
20	MAX	chr3:138663637-138666899	K562	blood:	n/a	chr3:138666114-138666124
21	ELK1	chr3:138666548-138666698	K562	blood:	n/a	n/a
22	E2F6	chr3:138663622-138666590	K562	blood:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
23	SUZ12	chr3:138666430-138666921	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:138664892-138666622	Hela-S3	cervix:	n/a	n/a
25	MYC	chr3:138662705-138666843	K562	blood:	n/a	chr3:138666114-138666124
26	JUND	chr3:138665643-138666689	K562	blood:	n/a	chr3:138666034-138666043 chr3:138665890-138665899
27	ZNF143	chr3:138666468-138666624	K562	blood:	n/a	n/a
28	HCFC1	chr3:138664985-138666613	K562	blood:	n/a	n/a
29	POLR2A	chr3:138664905-138666591	K562	blood:	n/a	n/a
30	POLR2A	chr3:138666373-138666575	Hela-S3	cervix:	n/a	n/a
31	JUN	chr3:138664800-138666967	K562	blood:	n/a	chr3:138666034-138666043 chr3:138665890-138665899
32	MAZ	chr3:138665021-138666670	Hela-S3	cervix:	n/a	chr3:138666114-138666124
33	MAX	chr3:138663683-138666644	H1-hESC	embryonic stem cell:	n/a	chr3:138666114-138666124
34	MAFF	chr3:138666473-138666846	K562	blood:	n/a	n/a
35	HEY1	chr3:138664942-138666637	K562	blood:	n/a	chr3:138665812-138665827
36	POLR2A	chr3:138664918-138666587	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:138664736-138666880	K562	blood:	n/a	n/a
38	UBTF	chr3:138664735-138666913	K562	blood:	n/a	n/a
39	E2F6	chr3:138663731-138667013	K562	blood:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
40	E2F6	chr3:138663107-138666566	H1-hESC	embryonic stem cell:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
41	POLR2A	chr3:138664603-138666834	K562	blood:	n/a	n/a
42	BHLHE40	chr3:138665062-138666787	K562	blood:	n/a	chr3:138665604-138665620
43	GTF2B	chr3:138665686-138666614	K562	blood:	n/a	n/a
44	CTBP2	chr3:138663148-138666770	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:138664745-138666712	K562	blood:	n/a	n/a
46	POLR2A	chr3:138664901-138666764	Hela-S3	cervix:	n/a	n/a
47	SUZ12	chr3:138662343-138670118	NT2-D1	testis:	n/a	n/a
48	CBX3	chr3:138665775-138666607	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138552263..138555163-chr3:138665790..138667540,3	K562	blood:
2	chr3:138552568..138555141-chr3:138666105..138668600,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS22-3	chr3:138666454-138666849	NONHSAT092347

Variant related genes	Relation type
FOXL2	TF binding region
ENSG00000244578	TF binding region
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv877540	chr3:138645013-138670695	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv877541	chr3:138645013-138673922	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv877542	chr3:138645013-138750904	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv3338518	chr3:138663787-138666635	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv529311	chr3:138665250-138667190	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138662400-138666600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:138662800-138666600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr3:138663000-138666600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:138663000-138666600	Active TSS	Hela-S3	cervix
5	chr3:138663400-138666600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:138663600-138666600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:138663600-138666600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr3:138663600-138666800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:138664200-138666600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:138664400-138666600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:138664400-138666600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:138664400-138666800	Active TSS	NHDF-Ad	bronchial
13	chr3:138664600-138666600	Active TSS	K562	blood
14	chr3:138664600-138668800	Active TSS	Ovary	ovary
15	chr3:138664800-138666600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:138664800-138666600	Active TSS	A549	lung
17	chr3:138665000-138666600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr3:138665000-138666600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:138665000-138666600	Bivalent Enhancer	Fetal Heart	heart
20	chr3:138665400-138666600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:138665400-138666800	Bivalent Enhancer	Liver	Liver
22	chr3:138665800-138666600	Bivalent/Poised TSS	HepG2	liver
23	chr3:138666000-138666600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr3:138666000-138666800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
25	chr3:138666000-138666800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
26	chr3:138666200-138666600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:138666200-138666600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr3:138666200-138666600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
29	chr3:138666200-138666800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:138666200-138666800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr3:138666200-138666800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
32	chr3:138666200-138666800	Enhancers	Gastric	stomach
33	chr3:138666200-138666800	Enhancers	Pancreas	Pancrea
34	chr3:138666200-138666800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
35	chr3:138666400-138666600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:138666400-138666600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
37	chr3:138666400-138666600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:138666400-138666600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:138666400-138666600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:138666400-138666600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
41	chr3:138666400-138666600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:138666400-138666600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:138666400-138666600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:138666400-138666600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
45	chr3:138666400-138666600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr3:138666400-138666600	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr3:138666400-138666600	Bivalent Enhancer	Fetal Stomach	stomach
48	chr3:138666400-138666600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr3:138666400-138666800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
50	chr3:138666400-138666800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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