Variant report

Variant	rs16963977
Chromosome Location	chr15:51203171-51203172
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr15:51202383-51203673	IMR90	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51202456..51205148-chr15:51207377..51210449,3	MCF-7	breast:
2	chr15:51201141..51202699-chr15:51202955..51205782,2	K562	blood:
3	chr15:51201141..51203041-chr15:51203150..51205782,2	K562	blood:
4	chr15:51199131..51202323-chr15:51202549..51205945,5	MCF-7	breast:
5	chr15:50645553..50650972-chr15:51199033..51203961,11	MCF-7	breast:

No data

Variant related genes	Relation type
AP4E1	TF binding region
ENSG00000104064	Chromatin interaction
ENSG00000081014	Chromatin interaction
ENSG00000244879	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11070815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631037	0.92[EUR][1000 genomes]
rs11633226	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755423	0.92[ASN][1000 genomes]
rs3759808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3886394	0.83[EUR][1000 genomes]
rs4775912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775914	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289295	0.82[EUR][1000 genomes]
rs7170736	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs72742336	0.82[EUR][1000 genomes]
rs72742362	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742383	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72744339	0.92[EUR][1000 genomes]
rs8038013	1.00[JPT][hapmap]
rs9806270	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1042372	chr15:50846461-51208891	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv542386	chr15:50846461-51208891	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv516168	chr15:51114437-51217361	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 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	chr15:51201400-51203800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr15:51201600-51203200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:51201600-51212000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:51201600-51243200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:51201600-51245000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:51201800-51203200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr15:51201800-51203200	Enhancers	Lung	lung
8	chr15:51201800-51203800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:51201800-51203800	Enhancers	NH-A	brain
10	chr15:51201800-51204200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:51201800-51204200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:51201800-51204200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:51201800-51204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:51201800-51204400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:51201800-51204400	Enhancers	Primary hematopoietic stem cells	blood
16	chr15:51201800-51204400	Weak transcription	Ovary	ovary
17	chr15:51201800-51204600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:51201800-51205000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:51201800-51205000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:51201800-51208200	Weak transcription	Brain Anterior Caudate	brain
21	chr15:51201800-51209200	Weak transcription	Stomach Mucosa	stomach
22	chr15:51201800-51209600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:51201800-51212600	Weak transcription	Aorta	Aorta
24	chr15:51201800-51223200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:51201800-51230600	Weak transcription	K562	blood
26	chr15:51201800-51242800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:51201800-51248400	Weak transcription	Colonic Mucosa	Colon
28	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:51202000-51203800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:51202000-51204000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:51202000-51204200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:51202000-51204200	Weak transcription	HepG2	liver
33	chr15:51202000-51204400	Enhancers	Primary B cells from cord blood	blood
34	chr15:51202000-51204600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr15:51202000-51204600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:51202000-51205000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:51202000-51207000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:51202000-51208200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:51202000-51212600	Weak transcription	Psoas Muscle	Psoas
40	chr15:51202000-51212800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:51202000-51217200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:51202000-51219000	Weak transcription	Right Ventricle	heart
43	chr15:51202200-51203200	Enhancers	Pancreas	Pancrea
44	chr15:51202200-51203400	Weak transcription	Primary T cells from cord blood	blood
45	chr15:51202200-51203600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr15:51202200-51203600	Weak transcription	Fetal Stomach	stomach
47	chr15:51202200-51203600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr15:51202200-51203600	Enhancers	NHLF	lung
49	chr15:51202200-51204200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:51202200-51204400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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