Variant report

Variant	rs11629776
Chromosome Location	chr15:42376451-42376452
allele	A/G
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	CTCF	chr15:42376416-42377152	A549	lung:	n/a	chr15:42376752-42376770 chr15:42376930-42376943 chr15:42376753-42376769 chr15:42376540-42376548
2	CTCF	chr15:42376422-42376527	GM19239	blood:	n/a	n/a
3	CTCF	chr15:42376414-42376531	GM12891	blood:	n/a	n/a
4	CTCF	chr15:42376396-42376541	GM19238	blood:	n/a	n/a
5	CTCF	chr15:42376451-42377179	HCT-116	colon:	n/a	chr15:42376752-42376770 chr15:42376930-42376943 chr15:42376753-42376769 chr15:42376540-42376548
6	CTCF	chr15:42376420-42376539	GM12892	blood:	n/a	n/a
7	RAD21	chr15:42376381-42377164	HCT-116	colon:	n/a	chr15:42376493-42376506 chr15:42377075-42377088
8	CTCF	chr15:42376340-42376490	K562	blood:	n/a	n/a
9	RAD21	chr15:42376379-42377157	HCT-116	colon:	n/a	chr15:42376493-42376506 chr15:42377075-42377088
10	CTCF	chr15:42376441-42376552	GM19240	blood:	n/a	chr15:42376540-42376548
11	CTCF	chr15:42376360-42376510	GM12872	blood:	n/a	n/a
12	CTCF	chr15:42376433-42377126	K562	blood:	n/a	chr15:42376752-42376770 chr15:42376930-42376943 chr15:42376753-42376769 chr15:42376540-42376548
13	SMC3	chr15:42376018-42377093	SK-N-SH	brain:	n/a	chr15:42376754-42376768
14	RAD21	chr15:42376369-42377062	ECC-1	luminal epithelium:	n/a	chr15:42376493-42376506
15	RAD21	chr15:42376352-42377178	SK-N-SH	brain:	n/a	chr15:42376493-42376506 chr15:42377075-42377088

No.	Distal block	Cell Line	Cell type
1	chr15:42196472..42197471-chr15:42376282..42376802,2	K562	blood:
2	chr15:42376332..42377032-chr15:42942436..42943073,2	MCF-7	breast:
3	chr15:42376241..42377224-chr15:42430049..42430612,3	K562	blood:
4	chr15:42360712..42361732-chr15:42376391..42377254,4	MCF-7	breast:
5	chr15:42281424..42281989-chr15:42376284..42377139,3	MCF-7	breast:

Variant related genes	Relation type
PLA2G4D	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10775125	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070359	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11635685	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11638531	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12902878	0.89[AFR][1000 genomes]
rs12906047	0.90[AFR][1000 genomes]
rs12906547	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1517555	0.86[AFR][1000 genomes]
rs1823551	0.84[ASN][1000 genomes]
rs2412657	0.86[ASN][1000 genomes]
rs4924612	0.83[AFR][1000 genomes]
rs4924618	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs938748	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1043641	chr15:42336584-42381240	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv904131	chr15:42343794-42390223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42369800-42385000	Weak transcription	Right Atrium	heart
2	chr15:42371800-42380800	Weak transcription	Pancreas	Pancrea
3	chr15:42372800-42383000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:42373200-42376800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:42373200-42376800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:42373400-42376800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:42373400-42376800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:42373400-42384400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:42373400-42384400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:42373600-42376800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:42373800-42376600	Weak transcription	Fetal Thymus	thymus
12	chr15:42375000-42376800	Enhancers	Fetal Muscle Leg	muscle
13	chr15:42375000-42377600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr15:42375000-42378200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:42375200-42380200	Weak transcription	Gastric	stomach
16	chr15:42375800-42377400	Enhancers	Esophagus	oesophagus
17	chr15:42375800-42377800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:42376200-42376800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:42376200-42376800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr15:42376200-42377000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:42376200-42377200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:42376200-42377400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr15:42376200-42377600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr15:42376400-42376600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:42376400-42376600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:42376400-42376600	Flanking Active TSS	Colonic Mucosa	Colon
27	chr15:42376400-42376600	Flanking Active TSS	Stomach Mucosa	stomach
28	chr15:42376400-42376800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
29	chr15:42376400-42376800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:42376400-42376800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
31	chr15:42376400-42376800	Active TSS	Hela-S3	cervix
32	chr15:42376400-42376800	Flanking Active TSS	HMEC	breast
33	chr15:42376400-42376800	Flanking Active TSS	NHEK	skin
34	chr15:42376400-42377000	Enhancers	Primary B cells from peripheral blood	blood
35	chr15:42376400-42377000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:42376400-42377000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr15:42376400-42377000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:42376400-42377000	Bivalent Enhancer	Brain Hippocampus Middle	brain
39	chr15:42376400-42377200	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr15:42376400-42377200	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr15:42376400-42377200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr15:42376400-42377200	Enhancers	Right Ventricle	heart
43	chr15:42376400-42377200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr15:42376400-42377400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr15:42376400-42377400	Enhancers	Fetal Intestine Large	intestine
46	chr15:42376400-42377400	Enhancers	Lung	lung
47	chr15:42376400-42377400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr15:42376400-42377600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:42376400-42377600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr15:42376400-42377600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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