Variant report

Variant	rs2862092
Chromosome Location	chr15:100025517-100025518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:100000166..100003019-chr15:100025458..100027654,2	MCF-7	breast:
2	chr15:99995946..99998218-chr15:100024533..100026194,2	K562	blood:
3	chr15:100024061..100027015-chr15:100105805..100107959,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2862093	0.92[ASN][1000 genomes]
rs2902137	0.92[ASN][1000 genomes]
rs7175649	0.82[CHB][hapmap]
rs748991	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs748992	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs755439	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs755440	0.89[ASN][1000 genomes]
rs874009	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs920655	0.87[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs930483	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]

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	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
2	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
3	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
4	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
5	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
6	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
7	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
8	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
9	nsv1050527	chr15:99983054-100035436	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv904558	chr15:100019382-100171684	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2862092	LYSMD4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100014800-100026800	Weak transcription	Aorta	Aorta
2	chr15:100018000-100026000	Weak transcription	A549	lung
3	chr15:100018200-100026000	Weak transcription	Stomach Mucosa	stomach
4	chr15:100018400-100025800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:100018400-100026800	Weak transcription	Gastric	stomach
6	chr15:100018600-100025600	Weak transcription	Right Ventricle	heart
7	chr15:100022000-100025600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:100022200-100026200	Weak transcription	HSMMtube	muscle
9	chr15:100024600-100026200	Enhancers	Fetal Stomach	stomach
10	chr15:100024600-100026400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:100024800-100025600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:100024800-100025800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:100024800-100026000	Weak transcription	Small Intestine	intestine
14	chr15:100025000-100027200	Enhancers	Fetal Heart	heart
15	chr15:100025200-100025800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr15:100025200-100025800	Enhancers	Thymus	Thymus
17	chr15:100025200-100026000	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr15:100025200-100026200	Enhancers	Primary B cells from peripheral blood	blood
19	chr15:100025200-100026200	Enhancers	Fetal Thymus	thymus
20	chr15:100025200-100026600	Enhancers	Spleen	Spleen
21	chr15:100025200-100027800	Enhancers	Lung	lung
22	chr15:100025400-100025600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr15:100025400-100025800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr15:100025400-100025800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:100025400-100025800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr15:100025400-100025800	Enhancers	Primary B cells from cord blood	blood
27	chr15:100025400-100025800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr15:100025400-100025800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:100025400-100025800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr15:100025400-100026000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:100025400-100026000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
32	chr15:100025400-100026000	Enhancers	Primary hematopoietic stem cells	blood
33	chr15:100025400-100026000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr15:100025400-100026000	Enhancers	Adipose Nuclei	Adipose
35	chr15:100025400-100026000	Enhancers	HepG2	liver
36	chr15:100025400-100026200	Enhancers	H9 Cell Line	embryonic stem cell
37	chr15:100025400-100026200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr15:100025400-100026200	Enhancers	Brain Angular Gyrus	brain
39	chr15:100025400-100026200	Enhancers	Brain Hippocampus Middle	brain
40	chr15:100025400-100026200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr15:100025400-100026200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr15:100025400-100026400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:100025400-100026400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr15:100025400-100026400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr15:100025400-100026400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr15:100025400-100026400	Enhancers	Fetal Muscle Trunk	muscle
47	chr15:100025400-100026400	Enhancers	Fetal Muscle Leg	muscle
48	chr15:100025400-100026600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:100025400-100026600	Enhancers	Left Ventricle	heart
50	chr15:100025400-100026600	Enhancers	Right Atrium	heart

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