Variant report

Variant	rs13087696
Chromosome Location	chr3:138313592-138313593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:388)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:388 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCB1	chr3:138312701-138313863	Hela-S3	cervix:	n/a	n/a
2	ELK1	chr3:138313545-138313799	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:138312502-138313785	K562	blood:	n/a	n/a
4	CTCF	chr3:138313560-138313710	GM06990	blood:	n/a	n/a
5	CBX3	chr3:138313178-138313841	K562	blood:	n/a	n/a
6	ZNF143	chr3:138312992-138313849	Hela-S3	cervix:	n/a	chr3:138313129-138313139
7	POLR2A	chr3:138312686-138313913	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr3:138312721-138313641	Hela-S3	cervix:	n/a	n/a
9	MAFK	chr3:138312980-138313934	HepG2	liver:	n/a	chr3:138313608-138313619 chr3:138313608-138313619
10	POLR2A	chr3:138312667-138313812	HUVEC	blood vessel:	n/a	n/a
11	WRNIP1	chr3:138313320-138314116	GM12878	blood:	n/a	n/a
12	CEBPB	chr3:138313079-138313998	HepG2	liver:	n/a	chr3:138313760-138313771
13	TAF1	chr3:138312765-138313800	H1-neurons	neurons:	n/a	n/a
14	CTCF	chr3:138313517-138313822	GM10266	blood:	n/a	n/a
15	CTCF	chr3:138313328-138313897	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr3:138313580-138313730	HMF	breast:	n/a	n/a
17	ZEB1	chr3:138312775-138313733	GM12878	blood:	n/a	chr3:138312965-138312972
18	MAZ	chr3:138312992-138313813	HepG2	liver:	n/a	chr3:138313244-138313254
19	RFX5	chr3:138312732-138313885	HepG2	liver:	n/a	chr3:138313432-138313448
20	HCFC1	chr3:138312835-138313856	K562	blood:	n/a	n/a
21	HEY1	chr3:138312743-138313627	HepG2	liver:	n/a	n/a
22	SIN3AK20	chr3:138312739-138313762	PANC-1	pancreas:	n/a	n/a
23	CTCF	chr3:138313582-138313760	A549	lung:	n/a	n/a
24	MAX	chr3:138312869-138313923	H1-hESC	embryonic stem cell:	n/a	chr3:138313687-138313697 chr3:138313244-138313254
25	POLR2A	chr3:138312848-138313715	K562	blood:	n/a	n/a
26	JUND	chr3:138312890-138313905	K562	blood:	n/a	chr3:138313270-138313279
27	POLR2A	chr3:138312744-138313791	ECC-1	luminal epithelium:	n/a	n/a
28	HEY1	chr3:138312445-138313774	K562	blood:	n/a	n/a
29	CTCF	chr3:138313265-138313835	Fibrobl	skin:	n/a	n/a
30	SIN3A	chr3:138312940-138313777	GM12878	blood:	n/a	n/a
31	YY1	chr3:138313520-138313855	A549	lung:	n/a	n/a
32	RAD21	chr3:138313553-138313837	K562	blood:	n/a	n/a
33	CTCF	chr3:138313560-138313710	HFF-Myc	foreskin:	n/a	n/a
34	PML	chr3:138312815-138313742	K562	blood:	n/a	n/a
35	CHD2	chr3:138312927-138313966	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr3:138312688-138313640	Gliobla	brain:	n/a	n/a
37	CTCF	chr3:138313044-138313964	Spleen_OC	spleen:	n/a	chr3:138313247-138313260
38	POLR2A	chr3:138312537-138313936	PANC-1	pancreas:	n/a	n/a
39	RAD21	chr3:138313340-138313954	Hela-S3	cervix:	n/a	n/a
40	CUX1	chr3:138313579-138313823	GM12878	blood:	n/a	n/a
41	YY1	chr3:138313509-138313834	HepG2	liver:	n/a	n/a
42	CTCF	chr3:138313302-138313837	ProgFib	skin:	n/a	n/a
43	POLR2A	chr3:138312553-138313837	GM18951	blood:	n/a	n/a
44	CTCF	chr3:138313478-138313889	A549	lung:	n/a	n/a
45	USF2	chr3:138313336-138313844	H1-hESC	embryonic stem cell:	n/a	chr3:138313687-138313698
46	CEBPB	chr3:138313111-138314041	K562	blood:	n/a	chr3:138313760-138313771
47	CTCF	chr3:138313330-138313840	GM19238	blood:	n/a	n/a
48	CTCF	chr3:138313508-138313813	Pancreas_OC	pancreas:	n/a	n/a
49	MTA3	chr3:138313175-138313959	GM12878	blood:	n/a	n/a
50	REST	chr3:138312370-138314124	H1-neurons	neurons:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:138309173..138314814-chr3:138323140..138328328,8	K562	blood:
2	chr3:138313052..138315422-chr3:138326245..138328582,4	MCF-7	breast:
3	chr3:138312852..138313723-chr7:123388941..123389568,2	Hela-S3	cervix:
4	chr16:88877584..88878443-chr3:138313223..138314081,2	Hela-S3	cervix:
5	chr3:138311550..138315468-chr3:138324471..138329332,12	MCF-7	breast:
6	chr3:138308688..138311077-chr3:138311353..138314105,2	MCF-7	breast:
7	chr3:138312690..138314858-chr3:138552284..138553853,2	K562	blood:
8	chr1:155658615..155659548-chr3:138312824..138313654,2	Hela-S3	cervix:
9	chr3:137892183..137893942-chr3:138313140..138314743,2	K562	blood:
10	chr3:138312928..138314956-chr3:138381208..138383898,2	K562	blood:

No data

Variant related genes	Relation type
CEP70	TF binding region
ENSG00000138231	Chromatin interaction
ENSG00000051382	Chromatin interaction
ENSG00000158234	Chromatin interaction
ENSG00000132676	Chromatin interaction
ENSG00000114107	Chromatin interaction
ENSG00000272686	Chromatin interaction
ENSG00000163374	Chromatin interaction
ENSG00000106299	Chromatin interaction
ENSG00000198931	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs34096688	1.00[AFR][1000 genomes]
rs34173962	1.00[AFR][1000 genomes]
rs3729781	1.00[LWK][hapmap]
rs3729782	1.00[GIH][hapmap]
rs66470363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66717475	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6772467	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	esv3429877	chr3:138272946-138325019	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr3:138310400-138313800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:138311400-138313800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:138311600-138313800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:138311600-138313800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:138311600-138315000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:138311800-138313600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr3:138311800-138313600	Active TSS	Brain Anterior Caudate	brain
8	chr3:138311800-138313800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:138311800-138313800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:138311800-138313800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:138311800-138313800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:138311800-138313800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:138311800-138313800	Active TSS	Rectal Smooth Muscle	rectum
14	chr3:138311800-138314000	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr3:138311800-138314000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr3:138312000-138313800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:138312000-138313800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr3:138312000-138313800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:138312000-138313800	Active TSS	Liver	Liver
20	chr3:138312000-138313800	Active TSS	Colonic Mucosa	Colon
21	chr3:138312000-138313800	Active TSS	Pancreas	Pancrea
22	chr3:138312000-138314000	Active TSS	Fetal Brain Female	brain
23	chr3:138312000-138314000	Active TSS	Fetal Kidney	kidney
24	chr3:138312200-138313600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:138312200-138313800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr3:138312200-138313800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:138312200-138313800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:138312200-138313800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:138312200-138313800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:138312200-138313800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:138312200-138313800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:138312200-138313800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:138312200-138313800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:138312200-138313800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:138312200-138313800	Active TSS	Fetal Intestine Large	intestine
36	chr3:138312200-138314000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr3:138312400-138313600	Active TSS	Gastric	stomach
38	chr3:138312400-138313600	Active TSS	Lung	lung
39	chr3:138312400-138313800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:138312400-138313800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:138312400-138313800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:138312400-138313800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:138312400-138313800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr3:138312400-138313800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:138312400-138313800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr3:138312400-138313800	Active TSS	Brain Angular Gyrus	brain
47	chr3:138312400-138313800	Active TSS	Brain Substantia Nigra	brain
48	chr3:138312400-138313800	Active TSS	Fetal Heart	heart
49	chr3:138312400-138313800	Active TSS	Fetal Muscle Trunk	muscle
50	chr3:138312400-138313800	Active TSS	Left Ventricle	heart

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