Variant report

Variant	rs11852686
Chromosome Location	chr15:74715205-74715206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74715058..74717919-chr15:74753629..74755415,2	K562	blood:
2	chr15:74712692..74714612-chr15:74714775..74716965,2	MCF-7	breast:
3	chr15:74711559..74715833-chr15:74724252..74727151,6	K562	blood:
4	chr15:74713352..74715766-chr15:74724000..74726928,3	MCF-7	breast:
5	chr15:74680306..74681854-chr15:74712615..74715350,2	MCF-7	breast:
6	chr15:74715079..74717127-chr15:74720885..74723638,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247240	Chromatin interaction
ENSG00000138623	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11856835	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12903353	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12909047	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12910841	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12916871	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16968740	1.00[CHB][hapmap]
rs750607	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription 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	58 gene(s)	inside rSNPs	diseases
3	nsv904352	chr15:74638965-74715205	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904353	chr15:74697084-74716609	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv904354	chr15:74697084-74722924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv904355	chr15:74697084-74728149	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv904356	chr15:74697084-74729603	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv569974	chr15:74701200-74727113	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv904357	chr15:74707993-74716609	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv904358	chr15:74708461-74716609	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv569976	chr15:74709071-74715211	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv904360	chr15:74709071-74728149	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
13	nsv569979	chr15:74709405-74722924	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv904364	chr15:74709975-74728149	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	nsv904366	chr15:74710125-74716609	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv569982	chr15:74710125-74721969	Genic enhancers Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv904367	chr15:74710125-74728149	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
18	nsv904368	chr15:74711122-74728149	Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
19	nsv542433	chr15:74714265-74745033	Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11852686	ULK3	cis	multi-tissue	Pritchard
rs11852686	SCAMP5	cis	cerebellum	SCAN
rs11852686	C15orf28	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74699600-74716600	Weak transcription	Fetal Kidney	kidney
2	chr15:74707200-74722400	Weak transcription	Fetal Intestine Small	intestine
3	chr15:74707800-74718000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:74708000-74717600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:74708400-74722400	Genic enhancers	Fetal Thymus	thymus
6	chr15:74709000-74715400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:74709000-74717600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:74709200-74720200	Weak transcription	Esophagus	oesophagus
9	chr15:74709200-74720800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr15:74709200-74724800	Weak transcription	Primary T cells from cord blood	blood
11	chr15:74709400-74716000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:74709400-74718000	Enhancers	HSMMtube	muscle
13	chr15:74709600-74718200	Enhancers	HMEC	breast
14	chr15:74709800-74718000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:74710000-74722800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:74710200-74718200	Enhancers	NHDF-Ad	bronchial
17	chr15:74710200-74718400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:74710200-74722000	Weak transcription	Dnd41	blood
19	chr15:74710400-74716400	Enhancers	Brain Cingulate Gyrus	brain
20	chr15:74710400-74718200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:74710400-74721200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:74710400-74722800	Enhancers	Brain Hippocampus Middle	brain
23	chr15:74711000-74718400	Enhancers	Brain Anterior Caudate	brain
24	chr15:74711000-74721000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:74711000-74723200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr15:74711000-74723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:74711400-74716400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:74711400-74717000	Enhancers	Fetal Brain Female	brain
29	chr15:74711400-74717600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr15:74711400-74719000	Enhancers	Placenta	Placenta
31	chr15:74711800-74716600	Enhancers	Primary B cells from peripheral blood	blood
32	chr15:74711800-74717800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr15:74712000-74715400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr15:74712000-74715600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr15:74712000-74716000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr15:74712200-74715600	Enhancers	Fetal Brain Male	brain
37	chr15:74712200-74716000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:74712200-74716400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:74712400-74716600	Enhancers	K562	blood
40	chr15:74712400-74717000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr15:74712400-74718000	Enhancers	Ovary	ovary
42	chr15:74712600-74715800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:74712600-74715800	Enhancers	Brain Germinal Matrix	brain
44	chr15:74712600-74716000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:74712600-74716200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr15:74712600-74716600	Enhancers	Right Atrium	heart
47	chr15:74712600-74716800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:74712600-74717600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:74712600-74718200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:74712800-74716200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links