Variant report

Variant	rs12120293
Chromosome Location	chr1:158027147-158027148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12120913	1.00[AFR][1000 genomes]
rs12121552	1.00[AFR][1000 genomes]
rs72711942	1.00[AFR][1000 genomes]
rs72711951	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1005196	chr1:158015996-158065522	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv523208	chr1:158022217-158088687	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1003592	chr1:158024499-158061043	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12120293	LELP1	cis	parietal	SCAN
rs12120293	RXFP4	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157997600-158047600	Weak transcription	Dnd41	blood
2	chr1:158001200-158047400	Weak transcription	Thymus	Thymus
3	chr1:158015200-158036400	Weak transcription	Esophagus	oesophagus
4	chr1:158015600-158029800	Weak transcription	Gastric	stomach
5	chr1:158016200-158030200	Weak transcription	Fetal Intestine Small	intestine
6	chr1:158016600-158028400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:158016800-158028000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:158016800-158028600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:158016800-158029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:158020200-158028400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:158020200-158034800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:158022800-158029000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:158023400-158035400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:158023600-158035000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:158023600-158036600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:158023600-158036800	Weak transcription	NH-A	brain
17	chr1:158023600-158048800	Weak transcription	A549	lung
18	chr1:158023800-158028000	Weak transcription	NHDF-Ad	bronchial
19	chr1:158023800-158033400	Weak transcription	HSMMtube	muscle
20	chr1:158024200-158027800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:158024200-158029800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:158024200-158030200	Strong transcription	HMEC	breast
23	chr1:158024400-158027800	Strong transcription	Osteobl	bone
24	chr1:158024400-158033800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:158024600-158027400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:158024600-158032000	Enhancers	Placenta	Placenta
27	chr1:158024800-158027200	Genic enhancers	Fetal Muscle Leg	muscle
28	chr1:158024800-158029200	Genic enhancers	Fetal Muscle Trunk	muscle
29	chr1:158024800-158030200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:158025000-158028600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:158025000-158029200	Weak transcription	Fetal Intestine Large	intestine
32	chr1:158025000-158030600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:158025000-158031400	Enhancers	Fetal Lung	lung
34	chr1:158025000-158031800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:158025000-158033800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:158025200-158027600	Enhancers	Fetal Heart	heart
37	chr1:158025200-158027800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:158025200-158028000	Strong transcription	NHLF	lung
39	chr1:158025200-158028200	Enhancers	HUVEC	blood vessel
40	chr1:158025200-158029200	Enhancers	Ovary	ovary
41	chr1:158025600-158028400	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr1:158025600-158030800	Genic enhancers	Fetal Stomach	stomach
43	chr1:158025600-158031200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:158025800-158027200	Weak transcription	NHEK	skin
45	chr1:158025800-158028800	Weak transcription	Fetal Kidney	kidney
46	chr1:158025800-158029000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:158025800-158029600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:158025800-158050000	Weak transcription	Hela-S3	cervix
49	chr1:158026000-158027200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:158026000-158027400	Weak transcription	Brain Germinal Matrix	brain

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