Variant report

Variant	rs2251889
Chromosome Location	chr15:44838835-44838836
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	IRF4	chr15:44838215-44838968	GM12878	blood:	n/a	n/a
2	YY1	chr15:44838603-44838891	GM12892	blood:	n/a	chr15:44838870-44838878 chr15:44838786-44838794
3	FOS	chr15:44838525-44838873	MCF10A-Er-Src	breast:	n/a	n/a
4	RUNX3	chr15:44837966-44838982	GM12878	blood:	n/a	n/a
5	FOS	chr15:44838547-44838916	MCF10A-Er-Src	breast:	n/a	n/a
6	IRF4	chr15:44838488-44838919	GM12878	blood:	n/a	n/a
7	ATF2	chr15:44838187-44838880	GM12878	blood:	n/a	n/a
8	ATF2	chr15:44838122-44839018	GM12878	blood:	n/a	n/a
9	YY1	chr15:44838680-44838978	SK-N-SH_RA	brain:	n/a	chr15:44838870-44838878 chr15:44838786-44838794
10	EP300	chr15:44838605-44839004	SK-N-SH_RA	brain:	n/a	n/a
11	EP300	chr15:44837820-44839443	SK-N-SH	brain:	n/a	n/a
12	FOS	chr15:44838597-44838896	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr15:44838567-44838920	MCF10A-Er-Src	breast:	n/a	n/a
14	MEF2C	chr15:44838160-44838957	GM12878	blood:	n/a	chr15:44838323-44838332 chr15:44838318-44838339 chr15:44838322-44838333 chr15:44838318-44838339 chr15:44838319-44838335 chr15:44838320-44838334 chr15:44838320-44838335
15	YY1	chr15:44838623-44838985	K562	blood:	n/a	chr15:44838870-44838878 chr15:44838786-44838794
16	TCF12	chr15:44838432-44839234	SK-N-SH	brain:	n/a	n/a
17	USF2	chr15:44838785-44838840	Hela-S3	cervix:	n/a	n/a
18	PBX3	chr15:44838561-44839049	SK-N-SH	brain:	n/a	n/a
19	PAX5	chr15:44838606-44838862	GM12878	blood:	n/a	n/a
20	PBX3	chr15:44838629-44839017	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr15:44838800-44838950	AoAF	blood vessel:	n/a	n/a
22	CEBPB	chr15:44838580-44838864	IMR90	lung:	n/a	n/a
23	NFIC	chr15:44838102-44838989	GM12878	blood:	n/a	n/a
24	MXI1	chr15:44837872-44839237	SK-N-SH	brain:	n/a	n/a
25	EBF1	chr15:44838560-44838928	GM12878	blood:	n/a	n/a
26	ZNF384	chr15:44838752-44839109	GM12878	blood:	n/a	n/a
27	EP300	chr15:44838603-44839080	SK-N-SH_RA	brain:	n/a	n/a
28	RUNX3	chr15:44838257-44838928	GM12878	blood:	n/a	n/a
29	BATF	chr15:44838257-44838915	GM12878	blood:	n/a	n/a
30	BCL11A	chr15:44838296-44838896	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:44838627-44839053	SK-N-SH	brain:	n/a	n/a
32	YY1	chr15:44838663-44838895	GM12878	blood:	n/a	chr15:44838870-44838878 chr15:44838786-44838794
33	CTCF	chr15:44838760-44838910	HEEpiC	esophagus:	n/a	n/a
34	TCF12	chr15:44838597-44839207	SK-N-SH	brain:	n/a	n/a
35	YY1	chr15:44838629-44838972	SK-N-SH_RA	brain:	n/a	chr15:44838870-44838878 chr15:44838786-44838794
36	YY1	chr15:44838656-44838938	GM12891	blood:	n/a	chr15:44838870-44838878 chr15:44838786-44838794
37	POLR2A	chr15:44838565-44838969	GM12891	blood:	n/a	n/a
38	EBF1	chr15:44838574-44838931	GM12878	blood:	n/a	n/a
39	SP1	chr15:44838514-44838883	GM12878	blood:	n/a	n/a
40	GATA3	chr15:44838552-44839089	SK-N-SH	brain:	n/a	n/a
41	EBF1	chr15:44838609-44838983	GM12878	blood:	n/a	n/a
42	BATF	chr15:44838568-44838931	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44798357..44800226-chr15:44837362..44838908,2	K562	blood:
2	chr15:44837165..44842769-chr15:44844512..44848405,4	MCF-7	breast:
3	chr15:44827352..44831205-chr15:44837293..44840798,4	MCF-7	breast:

Variant related genes	Relation type
EIF3J	TF binding region
ENSG00000104131	Chromatin interaction
ENSG00000179523	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16964417	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1863755	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2555346	1.00[ASW][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2556568	0.82[ASW][hapmap]
rs28656431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4611428	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6493107	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73417545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8026845	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[AFR][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	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44830400-44844000	Weak transcription	Lung	lung
2	chr15:44830400-44844400	Weak transcription	Spleen	Spleen
3	chr15:44830400-44848600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:44830400-44850200	Weak transcription	Aorta	Aorta
5	chr15:44830400-44855200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:44830400-44855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:44830800-44840400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:44830800-44844400	Weak transcription	Colonic Mucosa	Colon
9	chr15:44831000-44844000	Weak transcription	Thymus	Thymus
10	chr15:44831000-44844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:44831000-44844800	Weak transcription	Right Ventricle	heart
12	chr15:44831000-44856800	Weak transcription	Fetal Brain Male	brain
13	chr15:44832800-44840200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:44833000-44844400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:44833600-44844800	Weak transcription	Fetal Lung	lung
16	chr15:44833800-44840600	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:44833800-44843200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:44833800-44843800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:44833800-44844000	Weak transcription	Placenta	Placenta
20	chr15:44833800-44844600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:44833800-44857200	Weak transcription	Small Intestine	intestine
22	chr15:44834000-44844000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:44834000-44844400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:44834200-44840600	Weak transcription	Fetal Thymus	thymus
25	chr15:44834200-44844600	Weak transcription	Brain Substantia Nigra	brain
26	chr15:44834200-44844800	Weak transcription	Fetal Kidney	kidney
27	chr15:44834400-44840600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:44834400-44843200	Weak transcription	Fetal Intestine Large	intestine
29	chr15:44834400-44843400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:44834600-44843400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:44834600-44844400	Weak transcription	Fetal Brain Female	brain
32	chr15:44834600-44846200	Weak transcription	Brain Germinal Matrix	brain
33	chr15:44834800-44843200	Weak transcription	Dnd41	blood
34	chr15:44834800-44843200	Weak transcription	NHEK	skin
35	chr15:44835000-44840200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:44835000-44844000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:44835000-44844800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:44835000-44847200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:44835200-44840600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:44835200-44844800	Weak transcription	HepG2	liver
41	chr15:44835600-44843800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:44835600-44844600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:44835800-44844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:44836000-44840000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:44836000-44844800	Weak transcription	Ovary	ovary
46	chr15:44836200-44840200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:44836200-44840600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:44836600-44844000	Weak transcription	Gastric	stomach
49	chr15:44837000-44839000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr15:44837000-44840000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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