Variant report

Variant	rs2371978
Chromosome Location	chr12:59472972-59472973
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10506354	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444089	0.81[EUR][1000 genomes]
rs1444098	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1822586	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967546	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2197333	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2203085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218412	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2218413	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2371977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581229	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6650225	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7138934	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958198	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894906	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][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	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1047257	chr12:59444966-59520330	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050662	chr12:59444966-59526442	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2371978	RDH16	cis	parietal	SCAN
rs2371978	NDUFA4L2	cis	cerebellum	SCAN
rs2371978	OR6C68	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59465800-59478000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:59468400-59489000	Weak transcription	Esophagus	oesophagus
3	chr12:59468600-59473000	Enhancers	Fetal Lung	lung
4	chr12:59468800-59474200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr12:59470000-59474400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:59470200-59474400	Enhancers	Stomach Mucosa	stomach
7	chr12:59470600-59473400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:59470800-59473200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:59471400-59473000	Enhancers	HUVEC	blood vessel
10	chr12:59471600-59477000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:59471800-59477600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:59471800-59478800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:59471800-59480000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:59472000-59474200	Enhancers	HMEC	breast
15	chr12:59472000-59475400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:59472000-59476200	Weak transcription	Fetal Intestine Large	intestine
17	chr12:59472000-59477800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:59472000-59478200	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:59472200-59477000	Weak transcription	Fetal Stomach	stomach
20	chr12:59472200-59477400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:59472200-59477600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:59472200-59477600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:59472400-59473800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr12:59472600-59473800	Flanking Active TSS	NHEK	skin
25	chr12:59472600-59474000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr12:59472800-59473000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:59472800-59473000	Enhancers	Fetal Intestine Small	intestine
28	chr12:59472800-59473200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr12:59472800-59473200	Enhancers	Small Intestine	intestine
30	chr12:59472800-59473400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:59472800-59473400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:59472800-59473400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:59472800-59473600	Enhancers	Gastric	stomach

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