Variant report

Variant	rs882176
Chromosome Location	chr15:100268073-100268074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:100266948..100268782-chr15:100268887..100270856,3	MCF-7	breast:
2	chr15:100266137..100268275-chr15:100272075..100274209,4	MCF-7	breast:
3	chr15:100266755..100269601-chr15:100271373..100273805,2	K562	blood:

Variant related genes	Relation type
ENSG00000183060	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11247123	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1808723	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2061007	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2862867	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs325380	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6598265	0.82[JPT][hapmap]
rs882175	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921704	0.84[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
7	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers 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 target site	20 gene(s)	inside rSNPs	diseases
8	nsv428313	chr15:100236203-100757039	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv904563	chr15:100239546-100274747	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv570730	chr15:100240910-100700520	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	22 gene(s)	inside rSNPs	diseases
11	nsv1045838	chr15:100243067-101032218	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv904564	chr15:100245296-100723798	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv932678	chr15:100250311-101012358	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs882176	LYSMD4	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100244600-100272400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:100249600-100272800	Weak transcription	Small Intestine	intestine
3	chr15:100249800-100272200	Weak transcription	HUVEC	blood vessel
4	chr15:100251800-100271800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:100252200-100271400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:100253000-100271800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:100253200-100268400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:100253600-100268200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:100253600-100272400	Weak transcription	Stomach Mucosa	stomach
10	chr15:100255400-100269000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:100255800-100268400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:100257000-100268200	Weak transcription	Gastric	stomach
13	chr15:100257200-100268400	Weak transcription	Liver	Liver
14	chr15:100257600-100270400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:100258000-100268200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:100258000-100268600	Weak transcription	Colonic Mucosa	Colon
17	chr15:100258000-100268600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:100258000-100272000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr15:100258400-100268200	Weak transcription	Brain Angular Gyrus	brain
20	chr15:100258600-100268400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:100259000-100268200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:100259200-100270200	Weak transcription	Fetal Kidney	kidney
23	chr15:100259400-100268400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:100259800-100268800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:100259800-100272200	Weak transcription	Osteobl	bone
26	chr15:100260000-100268200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:100260000-100270000	Weak transcription	NHDF-Ad	bronchial
28	chr15:100261000-100268200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:100261000-100268200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:100261200-100268800	Weak transcription	Fetal Lung	lung
31	chr15:100261600-100268200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:100261600-100269000	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:100261600-100272400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:100261800-100268400	Weak transcription	Right Ventricle	heart
35	chr15:100261800-100272000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:100261800-100272000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:100261800-100272600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:100262000-100268400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:100262000-100268400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:100262000-100268800	Weak transcription	Primary T cells from cord blood	blood
41	chr15:100262000-100272200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:100262000-100272400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:100262200-100268200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:100262200-100268200	Weak transcription	HepG2	liver
45	chr15:100262200-100268400	Weak transcription	Lung	lung
46	chr15:100262200-100268400	Weak transcription	Pancreas	Pancrea
47	chr15:100262200-100268600	Weak transcription	Dnd41	blood
48	chr15:100262200-100272400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:100262800-100268400	Weak transcription	NHEK	skin
50	chr15:100262800-100270000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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