Variant report

Variant	rs7997838
Chromosome Location	chr13:39261222-39261223
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	SP1	chr13:39260679-39261399	H1-hESC	embryonic stem cell:	n/a	chr13:39261037-39261046 chr13:39261030-39261041 chr13:39260835-39260849
2	POLR2A	chr13:39261105-39261427	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr13:39260776-39261499	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr13:39260409-39261686	ECC-1	luminal epithelium:	n/a	n/a
5	CHD2	chr13:39260502-39262120	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
6	RAD21	chr13:39260922-39261437	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr13:39260671-39261714	H1-hESC	embryonic stem cell:	n/a	n/a
8	ATF2	chr13:39260843-39261365	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr13:39260348-39262065	H1-hESC	embryonic stem cell:	n/a	n/a
10	NFYB	chr13:39260986-39261283	K562	blood:	n/a	chr13:39261073-39261086
11	CREB1	chr13:39260492-39261483	H1-hESC	embryonic stem cell:	n/a	n/a
12	JUND	chr13:39260851-39261416	H1-hESC	embryonic stem cell:	n/a	chr13:39261073-39261082
13	SP1	chr13:39260856-39261309	H1-hESC	embryonic stem cell:	n/a	chr13:39261037-39261046 chr13:39261030-39261041
14	CHD1	chr13:39260721-39261618	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
15	USF2	chr13:39260995-39261309	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr13:39260842-39261548	MCF-7	breast:	n/a	n/a
17	E2F4	chr13:39260619-39261253	MCF10A-Er-Src	breast:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
18	GTF2F1	chr13:39260601-39261588	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr13:39260206-39261986	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
20	ATF2	chr13:39260938-39261357	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF12	chr13:39260846-39261386	ECC-1	luminal epithelium:	n/a	chr13:39261108-39261115
22	POLR2A	chr13:39260772-39261448	H1-hESC	embryonic stem cell:	n/a	n/a
23	TEAD4	chr13:39260942-39261381	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3A	chr13:39260139-39262313	H1-hESC	embryonic stem cell:	n/a	chr13:39261307-39261320
25	TAF1	chr13:39260763-39261599	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr13:39260556-39261638	H1-hESC	embryonic stem cell:	n/a	n/a
27	GABPA	chr13:39261082-39261396	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3AK20	chr13:39259931-39261825	MCF-7	breast:	n/a	n/a
29	TAF1	chr13:39260458-39261731	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr13:39260091-39261370	MCF-7	breast:	n/a	chr13:39260787-39260796
31	SP2	chr13:39260851-39261281	H1-hESC	embryonic stem cell:	n/a	n/a
32	BRCA1	chr13:39261086-39261366	H1-hESC	embryonic stem cell:	n/a	n/a
33	SP2	chr13:39260895-39261387	H1-hESC	embryonic stem cell:	n/a	n/a
34	SP4	chr13:39260990-39261370	H1-hESC	embryonic stem cell:	n/a	chr13:39261030-39261041
35	SETDB1	chr13:39260078-39261495	U2OS	brain:	n/a	n/a
36	POLR2A	chr13:39260314-39262185	H1-hESC	embryonic stem cell:	n/a	n/a
37	YY1	chr13:39260515-39261439	H1-hESC	embryonic stem cell:	n/a	chr13:39260834-39260843 chr13:39261291-39261302 chr13:39261309-39261323 chr13:39260638-39260649 chr13:39261294-39261308
38	ZNF143	chr13:39260139-39262011	H1-hESC	embryonic stem cell:	n/a	chr13:39261180-39261198 chr13:39261345-39261355
39	NFYB	chr13:39260921-39261300	GM12878	blood:	n/a	chr13:39261073-39261086
40	NANOG	chr13:39261047-39261288	H1-hESC	embryonic stem cell:	n/a	n/a
41	PML	chr13:39260825-39261455	MCF-7	breast:	n/a	chr13:39261405-39261413
42	MAX	chr13:39260345-39262000	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
43	E2F6	chr13:39260491-39262274	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
44	MAX	chr13:39260171-39261492	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796
45	TAF1	chr13:39260745-39261601	ECC-1	luminal epithelium:	n/a	n/a
46	GATA3	chr13:39260857-39262108	MCF-7	breast:	n/a	n/a
47	KAP1	chr13:39260290-39261341	U2OS	brain:	n/a	n/a
48	PBX3	chr13:39260978-39261338	SK-N-SH	brain:	n/a	chr13:39261075-39261084
49	E2F6	chr13:39260737-39262112	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
50	MYC	chr13:39260893-39261278	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:39260551..39262193-chr6:28047138..28049723,2	MCF-7	breast:
2	chr13:39259930..39261837-chr13:39400225..39402249,2	MCF-7	breast:
3	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:

Variant related genes	Relation type
FREM2	TF binding region
ENSG00000225350	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction
ENSG00000272009	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11147726	0.92[AFR][1000 genomes]
rs11147727	0.92[AFR][1000 genomes]
rs11147728	0.92[AFR][1000 genomes]
rs17058420	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058430	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058443	0.99[AFR][1000 genomes]
rs17058452	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs17058513	0.88[AFR][1000 genomes]
rs41418944	0.82[AFR][1000 genomes]
rs56359648	0.83[AMR][1000 genomes]
rs57001791	0.92[AFR][1000 genomes]
rs59255961	0.91[AFR][1000 genomes]
rs59593155	1.00[AMR][1000 genomes]
rs59939899	0.92[AFR][1000 genomes]
rs60698466	0.85[AFR][1000 genomes]
rs6563630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7336865	0.99[AFR][1000 genomes]
rs7982877	1.00[AMR][1000 genomes]
rs7984183	0.85[AFR][1000 genomes]
rs7984232	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs7999409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8002488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9671014	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39259600-39261800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr13:39259600-39262000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr13:39259800-39261400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr13:39259800-39262000	Active TSS	Fetal Kidney	kidney
5	chr13:39260000-39261600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr13:39260000-39261600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:39260000-39261800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr13:39260000-39261800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:39260000-39261800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr13:39260000-39261800	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr13:39260000-39261800	Active TSS	Aorta	Aorta
12	chr13:39260000-39262000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr13:39260000-39262000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:39260000-39262000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr13:39260000-39262200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr13:39260000-39262200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:39260000-39262200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:39260200-39261400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr13:39260200-39261400	Active TSS	Ovary	ovary
20	chr13:39260200-39261400	Active TSS	Right Ventricle	heart
21	chr13:39260200-39261600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
22	chr13:39260200-39261600	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr13:39260200-39261800	Flanking Active TSS	Liver	Liver
24	chr13:39260200-39261800	Active TSS	Brain Hippocampus Middle	brain
25	chr13:39260200-39262000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr13:39260200-39262000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr13:39260200-39262000	Active TSS	Fetal Heart	heart
28	chr13:39260200-39262000	Active TSS	Psoas Muscle	Psoas
29	chr13:39260200-39262200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr13:39260200-39262200	Active TSS	Brain Angular Gyrus	brain
31	chr13:39260200-39262200	Active TSS	Brain Substantia Nigra	brain
32	chr13:39260200-39262200	Active TSS	Rectal Smooth Muscle	rectum
33	chr13:39260200-39262200	Active TSS	Right Atrium	heart
34	chr13:39260200-39262400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:39260200-39262400	Active TSS	H9 Cell Line	embryonic stem cell
36	chr13:39260200-39262400	Active TSS	Brain Anterior Caudate	brain
37	chr13:39260200-39262400	Active TSS	Colon Smooth Muscle	Colon
38	chr13:39260400-39261400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr13:39260400-39261400	Active TSS	Colonic Mucosa	Colon
40	chr13:39260400-39261400	Active TSS	Pancreas	Pancrea
41	chr13:39260400-39261400	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr13:39260400-39261800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr13:39260400-39261800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
44	chr13:39260400-39261800	Active TSS	Gastric	stomach
45	chr13:39260400-39261800	Active TSS	Left Ventricle	heart
46	chr13:39260400-39262000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr13:39260400-39262200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr13:39260400-39262200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:39260400-39262200	Bivalent/Poised TSS	Fetal Thymus	thymus
50	chr13:39260400-39262400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet

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