Variant report

Variant	rs12441582
Chromosome Location	chr15:74688587-74688588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74687672..74690218-chr15:74730086..74732383,2	K562	blood:
2	chr15:74687904..74690050-chr15:74721010..74722729,2	MCF-7	breast:
3	chr15:74687537..74689333-chr15:74700401..74702548,2	MCF-7	breast:
4	chr15:74688222..74690157-chr15:74695368..74697306,2	K562	blood:
5	chr15:74673950..74692681-chr15:74720825..74732493,46	MCF-7	breast:
6	chr15:74681754..74686818-chr15:74686850..74691835,9	K562	blood:
7	chr15:74687929..74690624-chr15:74905195..74907946,2	K562	blood:
8	chr15:74674020..74678319-chr15:74686843..74691927,9	MCF-7	breast:
9	chr15:74688261..74689838-chr15:74715380..74717091,2	K562	blood:
10	chr15:74687793..74691115-chr15:74691233..74693928,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000179335	Chromatin interaction
ENSG00000138623	Chromatin interaction
ENSG00000260919	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs35163659	0.80[AFR][1000 genomes]
rs4243086	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5015024	0.82[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs7175229	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv904351	chr15:74638965-74697084	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12441582	SEMA7A	cis	cerebellum	SCAN
rs12441582	NRG4	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74667400-74691200	Enhancers	Placenta	Placenta
2	chr15:74675800-74695800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr15:74677600-74689000	Weak transcription	Primary T cells from cord blood	blood
4	chr15:74680600-74691800	Enhancers	Fetal Thymus	thymus
5	chr15:74681600-74695600	Enhancers	Primary B cells from peripheral blood	blood
6	chr15:74681800-74688800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:74683600-74688600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:74683800-74690200	Enhancers	Fetal Muscle Leg	muscle
9	chr15:74684000-74689000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:74684000-74690200	Enhancers	HSMMtube	muscle
11	chr15:74684200-74688800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:74684200-74689200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr15:74684600-74689200	Weak transcription	Lung	lung
14	chr15:74685000-74688600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr15:74685000-74688600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr15:74685000-74695000	Enhancers	HSMM	muscle
17	chr15:74685000-74695400	Weak transcription	Fetal Lung	lung
18	chr15:74685400-74688800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:74685400-74694400	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:74685400-74699400	Weak transcription	Brain Substantia Nigra	brain
21	chr15:74685800-74688600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:74685800-74694600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:74685800-74694800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:74686600-74689600	Enhancers	K562	blood
25	chr15:74686600-74690800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr15:74686600-74690800	Enhancers	NHLF	lung
27	chr15:74686600-74691400	Enhancers	NHDF-Ad	bronchial
28	chr15:74686600-74694400	Enhancers	Osteobl	bone
29	chr15:74686800-74689400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr15:74686800-74690000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:74686800-74690800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:74686800-74691200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:74686800-74695200	Enhancers	Primary B cells from cord blood	blood
34	chr15:74687000-74689000	Enhancers	NHEK	skin
35	chr15:74687000-74689200	Weak transcription	Dnd41	blood
36	chr15:74687400-74690600	Enhancers	Spleen	Spleen
37	chr15:74687400-74690800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:74687400-74690800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:74687400-74691400	Flanking Active TSS	GM12878-XiMat	blood
40	chr15:74687400-74692200	Enhancers	Thymus	Thymus
41	chr15:74687400-74694200	Enhancers	HMEC	breast
42	chr15:74687400-74696200	Enhancers	NH-A	brain
43	chr15:74687600-74689600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:74687600-74690000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:74687600-74690600	Enhancers	Esophagus	oesophagus
46	chr15:74687800-74689400	Enhancers	Gastric	stomach
47	chr15:74687800-74690400	Enhancers	Stomach Mucosa	stomach
48	chr15:74687800-74690600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:74687800-74694000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:74688000-74689400	Enhancers	Fetal Intestine Small	intestine

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