Variant report

Variant	rs12916961
Chromosome Location	chr15:41151104-41151105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41150041..41152139-chr15:41152900..41156104,3	K562	blood:
2	chr15:41148610..41153040-chr15:41153153..41159814,9	MCF-7	breast:
3	chr15:41030818..41032817-chr15:41149511..41151476,2	K562	blood:
4	chr15:41148671..41154287-chr15:41183537..41188403,13	MCF-7	breast:
5	chr15:41140669..41146997-chr15:41148125..41153622,6	K562	blood:
6	chr15:41151059..41151968-chr15:41184909..41185645,2	MCF-7	breast:
7	chr15:41150583..41152026-chr15:41183523..41185167,5	K562	blood:
8	chr15:41149992..41152598-chr15:41170919..41172722,2	K562	blood:
9	chr15:41148526..41152420-chr15:41165640..41167925,3	K562	blood:
10	chr15:41149915..41158340-chr15:41160487..41168241,17	MCF-7	breast:
11	chr15:41137274..41141358-chr15:41148658..41151865,7	MCF-7	breast:
12	chr15:41055356..41057797-chr15:41150311..41151854,2	K562	blood:
13	chr15:41149030..41159900-chr15:41180834..41187281,18	MCF-7	breast:
14	chr15:41147027..41152625-chr15:41184304..41188925,8	K562	blood:
15	chr15:41150105..41152122-chr15:41152976..41154700,3	MCF-7	breast:
16	chr15:41150922..41152005-chr15:41185954..41186723,4	K562	blood:
17	chr15:41150722..41152078-chr15:41185908..41187003,9	MCF-7	breast:
18	chr15:41148133..41159834-chr15:41169228..41175193,12	MCF-7	breast:
19	chr15:41150681..41151918-chr15:41165518..41166393,6	MCF-7	breast:
20	chr15:41150944..41152426-chr15:41183613..41184775,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166145	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000264256	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11070298	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11070299	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11856227	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12148523	0.82[ASN][1000 genomes]
rs12903603	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16971157	1.00[CEU][hapmap]
rs1814692	0.88[EUR][1000 genomes]
rs2279578	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2412571	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28444382	0.81[EUR][1000 genomes]
rs4244581	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4384588	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4923885	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4923886	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4923887	0.81[EUR][1000 genomes]
rs4924509	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4924510	0.80[ASN][1000 genomes]
rs601436	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs617377	0.81[EUR][1000 genomes]
rs618892	0.92[CEU][hapmap]
rs625058	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs690507	0.84[EUR][1000 genomes]
rs7172280	1.00[CEU][hapmap]
rs8024861	1.00[CEU][hapmap]
rs8024961	1.00[CEU][hapmap]
rs8028660	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9806683	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41152200	Weak transcription	Small Intestine	intestine
2	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
3	chr15:41140400-41151200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:41140600-41151600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:41141200-41152600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41146600-41154200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:41147600-41151400	Genic enhancers	Rectal Mucosa Donor 29	rectum
8	chr15:41147800-41151600	Genic enhancers	Rectal Mucosa Donor 31	rectum
9	chr15:41148200-41151600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:41148400-41151400	Genic enhancers	Duodenum Mucosa	Duodenum
11	chr15:41148400-41151800	Genic enhancers	Fetal Intestine Small	intestine
12	chr15:41148600-41151600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:41149000-41154400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:41149200-41151600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:41149200-41151600	Enhancers	Fetal Thymus	thymus
16	chr15:41149400-41151200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:41149400-41151600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:41149400-41151600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr15:41149400-41151800	Enhancers	A549	lung
20	chr15:41149400-41154400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr15:41149400-41154600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr15:41149600-41151200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:41149600-41151400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:41149600-41151600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:41149600-41152000	Enhancers	K562	blood
26	chr15:41149600-41152600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:41149600-41158000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:41149800-41151200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:41149800-41151200	Strong transcription	Gastric	stomach
30	chr15:41149800-41151400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:41149800-41151600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:41149800-41151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:41149800-41152200	Enhancers	Pancreas	Pancrea
34	chr15:41149800-41152200	Enhancers	Stomach Mucosa	stomach
35	chr15:41149800-41158200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:41150000-41151200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr15:41150000-41151200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:41150000-41151200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr15:41150000-41154400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr15:41150000-41158200	Weak transcription	HMEC	breast
41	chr15:41150000-41165600	Weak transcription	Spleen	Spleen
42	chr15:41150200-41151200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr15:41150200-41151400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:41150200-41151400	Weak transcription	Liver	Liver
45	chr15:41150200-41151400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:41150200-41151400	Weak transcription	Placenta	Placenta
47	chr15:41150200-41151600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:41150200-41151600	Weak transcription	Brain Anterior Caudate	brain
49	chr15:41150400-41151200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:41150400-41151200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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