Variant report

Variant	rs3816717
Chromosome Location	chr15:51204133-51204134
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	EBF1	chr15:51203960-51204203	GM12878	blood:	n/a	chr15:51204081-51204090 chr15:51204079-51204090
2	SPI1	chr15:51203798-51204324	HL-60	blood:	n/a	chr15:51204021-51204030 chr15:51204042-51204055 chr15:51204046-51204053 chr15:51204018-51204031 chr15:51204019-51204032

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:

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

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10519289	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070825	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs11634895	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11636974	0.94[JPT][hapmap]
rs11639007	0.83[ASN][1000 genomes]
rs11639350	0.86[ASN][1000 genomes]
rs11853182	0.90[ASN][1000 genomes]
rs11854585	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11854729	0.82[ASN][1000 genomes]
rs11856609	0.90[ASN][1000 genomes]
rs11857981	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12324214	0.94[JPT][hapmap]
rs12324583	0.88[JPT][hapmap]
rs12441734	0.94[JPT][hapmap]
rs12898402	0.88[JPT][hapmap]
rs12899397	0.85[ASN][1000 genomes]
rs12899586	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12900916	0.85[ASN][1000 genomes]
rs12900973	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901608	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12902050	0.94[JPT][hapmap]
rs12903317	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904155	0.94[JPT][hapmap]
rs12906278	0.94[JPT][hapmap]
rs12907367	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12910854	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911270	0.88[JPT][hapmap]
rs12911715	0.85[ASN][1000 genomes]
rs12913094	0.85[ASN][1000 genomes]
rs12916255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1438926	0.94[JPT][hapmap]
rs16953045	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs16953046	0.85[ASN][1000 genomes]
rs16963993	0.80[YRI][hapmap]
rs17521467	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs17521789	0.82[ASN][1000 genomes]
rs17521919	0.82[ASN][1000 genomes]
rs17599863	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs17599974	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1904432	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2278559	0.88[JPT][hapmap]
rs2306329	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306333	0.85[ASN][1000 genomes]
rs28366661	0.80[ASN][1000 genomes]
rs28430533	0.82[ASN][1000 genomes]
rs28642856	0.83[ASN][1000 genomes]
rs34590712	0.88[ASN][1000 genomes]
rs34810611	0.88[ASN][1000 genomes]
rs35416047	0.82[ASN][1000 genomes]
rs35684604	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35827195	0.90[ASN][1000 genomes]
rs3759806	0.85[ASN][1000 genomes]
rs3825799	1.00[JPT][hapmap]
rs3848133	0.94[JPT][hapmap]
rs3848134	0.88[JPT][hapmap]
rs58661036	0.85[ASN][1000 genomes]
rs6493470	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71471523	0.83[ASN][1000 genomes]
rs71471583	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71471584	0.82[ASN][1000 genomes]
rs71471585	0.82[ASN][1000 genomes]
rs71471587	0.80[ASN][1000 genomes]
rs7162325	0.88[JPT][hapmap]
rs7162562	0.92[ASN][1000 genomes]
rs7162631	0.88[JPT][hapmap]
rs7165920	0.85[ASN][1000 genomes]
rs7170009	0.94[JPT][hapmap]
rs7170570	0.88[ASN][1000 genomes]
rs7170937	0.87[JPT][hapmap]
rs7175024	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs7179321	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7179865	0.94[JPT][hapmap]
rs7181081	0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026140	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8032236	0.85[ASN][1000 genomes]
rs8032550	0.82[ASN][1000 genomes]
rs8032866	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs8033015	0.89[JPT][hapmap]
rs8033085	0.88[JPT][hapmap]
rs8033351	0.88[JPT][hapmap]
rs8034718	0.88[JPT][hapmap]
rs8034812	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038437	0.94[JPT][hapmap]
rs8040954	0.88[JPT][hapmap]
rs9302158	0.94[JPT][hapmap]
rs9652426	0.85[ASN][1000 genomes]
rs9806654	0.88[JPT][hapmap]

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	chr15:51201600-51212000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:51201600-51243200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:51201600-51245000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:51201800-51204200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:51201800-51204200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:51201800-51204200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:51201800-51204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:51201800-51204400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:51201800-51204400	Enhancers	Primary hematopoietic stem cells	blood
10	chr15:51201800-51204400	Weak transcription	Ovary	ovary
11	chr15:51201800-51204600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:51201800-51205000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:51201800-51205000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:51201800-51208200	Weak transcription	Brain Anterior Caudate	brain
15	chr15:51201800-51209200	Weak transcription	Stomach Mucosa	stomach
16	chr15:51201800-51209600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:51201800-51212600	Weak transcription	Aorta	Aorta
18	chr15:51201800-51223200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:51201800-51230600	Weak transcription	K562	blood
20	chr15:51201800-51242800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:51201800-51248400	Weak transcription	Colonic Mucosa	Colon
22	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:51202000-51204200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:51202000-51204200	Weak transcription	HepG2	liver
25	chr15:51202000-51204400	Enhancers	Primary B cells from cord blood	blood
26	chr15:51202000-51204600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr15:51202000-51204600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:51202000-51205000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:51202000-51207000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:51202000-51208200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:51202000-51212600	Weak transcription	Psoas Muscle	Psoas
32	chr15:51202000-51212800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:51202000-51217200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:51202000-51219000	Weak transcription	Right Ventricle	heart
35	chr15:51202200-51204200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:51202200-51204400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:51202200-51204800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr15:51202200-51204800	Weak transcription	Fetal Intestine Large	intestine
39	chr15:51202200-51204800	Weak transcription	Fetal Intestine Small	intestine
40	chr15:51202200-51205200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr15:51202200-51205400	Weak transcription	Fetal Lung	lung
42	chr15:51202200-51207200	Weak transcription	Fetal Kidney	kidney
43	chr15:51202200-51210000	Weak transcription	Fetal Brain Female	brain
44	chr15:51202200-51210000	Weak transcription	Thymus	Thymus
45	chr15:51202200-51214200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:51202200-51222600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr15:51202400-51204800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:51202400-51205000	Weak transcription	Fetal Brain Male	brain
49	chr15:51202400-51205000	Weak transcription	Fetal Thymus	thymus
50	chr15:51202400-51209800	Weak transcription	Brain Inferior Temporal Lobe	brain

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