Variant report

Variant	rs4965459
Chromosome Location	chr15:99764444-99764445
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	chr15:99762009..99765655-chr15:99790108..99792308,4	MCF-7	breast:
2	chr15:99737190..99739756-chr15:99764410..99766560,2	K562	blood:

Variant related genes	Relation type
ENSG00000103852	Chromatin interaction
ENSG00000168904	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12912760	0.83[MEX][hapmap]
rs13853	0.83[CHD][hapmap]
rs260086	0.83[CHD][hapmap]
rs2602033	0.88[CHB][hapmap]
rs2602037	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs2623178	0.88[CHB][hapmap]
rs2623194	0.83[MEX][hapmap]
rs2665082	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap]
rs4965222	0.89[MEX][hapmap]
rs5030691	0.83[CHD][hapmap]
rs7162708	0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs7170268	0.83[CHD][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	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
9	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS 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	30 gene(s)	inside rSNPs	diseases
12	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
13	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
15	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
17	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4965459	LRRC28	cis	parietal	SCAN
rs4965459	TTC23	cis	Thyroid	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99724400-99769600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:99733400-99787400	Weak transcription	NHEK	skin
4	chr15:99749800-99789400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:99750000-99789400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:99751800-99768600	Strong transcription	Fetal Muscle Leg	muscle
7	chr15:99752800-99766800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:99753200-99766800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:99753400-99767000	Weak transcription	NHLF	lung
10	chr15:99754400-99768000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:99754400-99768600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:99754400-99768800	Strong transcription	Fetal Intestine Large	intestine
13	chr15:99754800-99769000	Strong transcription	Adipose Nuclei	Adipose
14	chr15:99755400-99768800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:99755600-99767800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:99755600-99768000	Strong transcription	Liver	Liver
17	chr15:99756200-99765000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:99756400-99765200	Strong transcription	Fetal Lung	lung
19	chr15:99756600-99768800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:99756600-99769000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:99756600-99789400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr15:99756800-99768800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:99756800-99768800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr15:99756800-99769000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:99757000-99768200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:99757600-99765800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:99757600-99768800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:99757800-99768600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:99757800-99768600	Strong transcription	Fetal Stomach	stomach
30	chr15:99757800-99768800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:99757800-99769000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:99758000-99765600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr15:99758000-99768800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr15:99758200-99769000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:99758400-99768000	Weak transcription	HMEC	breast
36	chr15:99758600-99765000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:99758600-99765200	Weak transcription	Psoas Muscle	Psoas
38	chr15:99758600-99766000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:99758600-99789400	Weak transcription	Brain Substantia Nigra	brain
40	chr15:99758800-99765400	Weak transcription	Colonic Mucosa	Colon
41	chr15:99758800-99768400	Weak transcription	Brain Angular Gyrus	brain
42	chr15:99759200-99764800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:99759200-99764800	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:99759200-99767800	Weak transcription	Fetal Brain Male	brain
45	chr15:99759200-99769800	Weak transcription	Brain Anterior Caudate	brain
46	chr15:99759200-99788400	Weak transcription	Fetal Thymus	thymus
47	chr15:99759400-99769200	Weak transcription	Primary T cells from cord blood	blood
48	chr15:99759400-99781800	Weak transcription	Spleen	Spleen
49	chr15:99759400-99788600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr15:99759400-99788600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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