Variant report

Variant	rs11635054
Chromosome Location	chr15:51237910-51237911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51237490..51239996-chr15:51331405..51333365,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLDN-5	chr15:51236326-51238762	NONHSAT042446
2	lnc-GLDN-5	chr15:51236860-51238193	NONHSAT042447

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11070815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631037	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11633226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441319	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963977	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]
rs2619684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755423	0.92[ASN][1000 genomes]
rs3759808	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3886394	0.81[EUR][1000 genomes]
rs4775912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775914	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289295	0.80[EUR][1000 genomes]
rs7170736	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[EUR][1000 genomes]
rs72742336	0.80[EUR][1000 genomes]
rs72742362	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742383	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72744339	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9806270	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569404	chr15:51234595-51294995	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51201600-51243200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:51201600-51245000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:51201800-51242800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:51201800-51248400	Weak transcription	Colonic Mucosa	Colon
5	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:51202600-51241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:51202600-51242800	Weak transcription	Gastric	stomach
8	chr15:51202800-51243400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:51203200-51242200	Weak transcription	Brain Substantia Nigra	brain
10	chr15:51203200-51242800	Weak transcription	Lung	lung
11	chr15:51203400-51242400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:51204800-51243000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:51205600-51242800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:51205800-51249000	Weak transcription	Fetal Brain Male	brain
15	chr15:51205800-51254400	Weak transcription	Fetal Heart	heart
16	chr15:51208000-51250400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:51208400-51242200	Weak transcription	Fetal Kidney	kidney
18	chr15:51210400-51243000	Weak transcription	Brain Angular Gyrus	brain
19	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
20	chr15:51213000-51242800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:51213200-51245400	Weak transcription	Psoas Muscle	Psoas
22	chr15:51213600-51243400	Weak transcription	Pancreas	Pancrea
23	chr15:51213800-51247600	Weak transcription	Aorta	Aorta
24	chr15:51214600-51247800	Weak transcription	Esophagus	oesophagus
25	chr15:51219800-51243000	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:51220000-51242200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:51220200-51243000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:51221800-51242200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:51221800-51242400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:51221800-51242800	Weak transcription	Brain Anterior Caudate	brain
31	chr15:51222000-51242800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:51223400-51243000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:51223400-51243000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:51225000-51242200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:51226000-51240600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:51226000-51242400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:51231000-51241200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:51231000-51241200	Weak transcription	Fetal Stomach	stomach
39	chr15:51231000-51242600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:51231000-51242800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:51231000-51242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:51231000-51243000	Weak transcription	Brain Germinal Matrix	brain
43	chr15:51231000-51247800	Weak transcription	Spleen	Spleen
44	chr15:51231200-51242600	Weak transcription	Fetal Brain Female	brain
45	chr15:51231200-51242800	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:51231200-51242800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:51232400-51243200	Weak transcription	Fetal Intestine Small	intestine
48	chr15:51232400-51250400	Weak transcription	HepG2	liver
49	chr15:51232800-51242800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:51232800-51254000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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