Variant report

Variant	rs12904353
Chromosome Location	chr15:51046618-51046619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50987564..50989809-chr15:51045515..51047081,2	MCF-7	breast:
2	chr15:51042311..51046863-chr15:51056466..51060433,4	MCF-7	breast:
3	chr15:50978651..50980490-chr15:51043656..51047241,4	K562	blood:
4	chr15:51039307..51042785-chr15:51044008..51048436,3	MCF-7	breast:
5	chr15:51045886..51047999-chr15:51058293..51060374,2	K562	blood:
6	chr15:51046404..51048794-chr15:51049414..51052213,2	K562	blood:

Variant related genes	Relation type
ENSG00000092439	Chromatin interaction
ENSG00000138600	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10519284	0.87[CEU][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1052459	0.87[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11635825	0.94[JPT][hapmap]
rs11854949	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11858096	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898588	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12899074	0.94[JPT][hapmap]
rs12899321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899580	0.80[ASN][1000 genomes]
rs12899700	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12899943	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12900933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12902399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12903573	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12904617	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904729	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12905120	0.92[JPT][hapmap]
rs12905720	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906675	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs12907387	1.00[JPT][hapmap]
rs12907472	0.94[JPT][hapmap]
rs12907922	0.94[JPT][hapmap]
rs12908546	0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910613	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911654	0.82[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12911753	0.88[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs12912192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12912835	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12912921	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12913081	0.94[JPT][hapmap]
rs12913494	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12913657	0.84[ASN][1000 genomes]
rs12913733	0.90[EUR][1000 genomes]
rs12914606	0.83[ASN][1000 genomes]
rs12915606	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12916113	0.93[JPT][hapmap]
rs12916122	0.80[ASN][1000 genomes]
rs12916510	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs12917462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16973487	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs28641162	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2928138	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs34885055	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35148930	0.80[ASN][1000 genomes]
rs35597009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485324	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs531366	0.93[JPT][hapmap]
rs540257	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs543821	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs555569	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs615835	0.94[JPT][hapmap]
rs623639	0.94[JPT][hapmap]
rs623652	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs646856	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs71397503	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71397504	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71397507	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71471514	0.80[AMR][1000 genomes]
rs71471515	0.80[AMR][1000 genomes]
rs7165492	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165684	0.93[JPT][hapmap]
rs7173321	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs8037161	0.94[JPT][hapmap]
rs8042919	0.94[JPT][hapmap]
rs9920083	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	65 gene(s)	inside rSNPs	diseases
2	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1051990	chr15:50745814-51133186	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv457134	chr15:50770868-51184583	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv471242	chr15:50770868-51184583	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS 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	54 gene(s)	inside rSNPs	diseases
9	nsv569396	chr15:50770868-51184583	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	nsv457135	chr15:50770868-51189707	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
11	nsv569397	chr15:50770868-51189707	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking 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	54 gene(s)	inside rSNPs	diseases
12	nsv1048621	chr15:50775451-51115535	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
13	nsv1047039	chr15:50782070-51187804	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv542385	chr15:50782070-51187804	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
15	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
16	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
17	nsv1036081	chr15:50818569-51097229	Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
18	nsv1055112	chr15:50822035-51133186	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	46 gene(s)	inside rSNPs	diseases
19	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
20	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
21	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
22	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
23	nsv904212	chr15:50979738-51132170	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
24	nsv904213	chr15:51011402-51119731	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	nsv1044320	chr15:51016364-51074061	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
26	nsv457137	chr15:51019117-51117524	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
27	nsv569402	chr15:51019117-51117524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50988000-51056800	Weak transcription	Esophagus	oesophagus
2	chr15:51004000-51056200	Weak transcription	Brain Angular Gyrus	brain
3	chr15:51022600-51047600	Weak transcription	Aorta	Aorta
4	chr15:51028600-51055400	Weak transcription	Dnd41	blood
5	chr15:51029800-51055200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:51031400-51056400	Weak transcription	Fetal Brain Female	brain
7	chr15:51032000-51056000	Weak transcription	HSMM	muscle
8	chr15:51033400-51049600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:51035600-51055400	Weak transcription	Primary T cells from cord blood	blood
10	chr15:51037800-51047600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:51038200-51047600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:51038200-51053400	Weak transcription	Spleen	Spleen
13	chr15:51038600-51056000	Weak transcription	Thymus	Thymus
14	chr15:51039200-51047400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:51039200-51053000	Weak transcription	Fetal Intestine Small	intestine
16	chr15:51039200-51055200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:51039600-51053400	Weak transcription	Left Ventricle	heart
18	chr15:51039600-51054600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:51039600-51054600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:51039600-51056200	Weak transcription	NH-A	brain
21	chr15:51039800-51055200	Weak transcription	Fetal Thymus	thymus
22	chr15:51039800-51056600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:51040000-51048000	Weak transcription	HSMMtube	muscle
24	chr15:51040000-51055200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:51040000-51056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:51040000-51056200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:51040000-51056200	Weak transcription	Brain Germinal Matrix	brain
28	chr15:51040200-51047600	Weak transcription	NHDF-Ad	bronchial
29	chr15:51040200-51047600	Weak transcription	Osteobl	bone
30	chr15:51040200-51056400	Weak transcription	Fetal Intestine Large	intestine
31	chr15:51040400-51054600	Weak transcription	Primary B cells from cord blood	blood
32	chr15:51040400-51056400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:51040400-51056800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:51041000-51056400	Weak transcription	Colonic Mucosa	Colon
35	chr15:51041200-51055200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:51041400-51054600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:51041400-51056000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:51041400-51056000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:51041600-51055200	Weak transcription	HepG2	liver
40	chr15:51041800-51048200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:51041800-51056800	Weak transcription	Brain Substantia Nigra	brain
42	chr15:51042000-51052400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:51042000-51054800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:51042000-51055200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:51042000-51055200	Weak transcription	Liver	Liver
46	chr15:51042000-51055400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:51042000-51056000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:51042000-51056000	Weak transcription	Placenta	Placenta
49	chr15:51042000-51056000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr15:51042000-51056200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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