Variant report

Variant	rs7138420
Chromosome Location	chr12:50583150-50583151
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50477100..50479136-chr12:50582674..50585443,2	K562	blood:
2	chr12:50574926..50577485-chr12:50582740..50584588,2	K562	blood:
3	chr12:50583119..50586019-chr12:50610359..50613018,3	K562	blood:
4	chr12:50581029..50583186-chr12:50589961..50592504,2	K562	blood:
5	chr12:50494779..50496770-chr12:50580930..50583247,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CERS5-1	chr12:50579363-50584044	ENSG00000257298.1

No data

Variant related genes	Relation type
ENSG00000257531	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10506292	0.96[CEU][hapmap]
rs10783338	0.83[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs10783344	0.96[CEU][hapmap]
rs10876000	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs10876014	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs10876015	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs10876017	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs10876023	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs10876024	0.95[CEU][hapmap]
rs11169281	0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap]
rs11169282	0.83[ASW][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap]
rs11169314	0.81[EUR][1000 genomes]
rs11169315	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11169322	0.96[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs11169331	0.96[CEU][hapmap]
rs11169332	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11169335	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11169348	0.96[CEU][hapmap]
rs11169350	0.96[CEU][hapmap]
rs11169351	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11169357	0.96[CEU][hapmap]
rs11169360	1.00[CEU][hapmap]
rs11169370	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11833608	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs11838347	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs12303082	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs12367872	0.96[CEU][hapmap];0.80[TSI][hapmap]
rs12422417	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs12424335	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12424691	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs12424713	0.96[CEU][hapmap]
rs12425705	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs12828340	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs1362983	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs1554844	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1554845	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs17124432	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs17124514	0.84[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2111988	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs2302900	0.91[CEU][hapmap]
rs2358539	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs34245511	0.92[ASN][1000 genomes]
rs3741562	0.83[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs3812825	0.96[CEU][hapmap]
rs4348979	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs4421818	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs4768951	0.92[CEU][hapmap]
rs6580736	0.92[CEU][hapmap]
rs6580738	0.92[CEU][hapmap]
rs7132551	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7134595	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7138622	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7138945	0.84[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap]
rs7294618	0.83[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7296291	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7307230	0.83[ASW][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7308474	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7311973	0.95[CEU][hapmap]
rs7312252	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7315690	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486747	0.96[CEU][hapmap]
rs7953953	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7961065	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7961112	0.83[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7972465	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7979830	0.96[CEU][hapmap]
rs9364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7138420	SLC38A1	cis	parietal	SCAN
rs7138420	CELA1	cis	parietal	SCAN
rs7138420	DIP2B	cis	cerebellum	SCAN
rs7138420	CERS5	cis	Nerve Tibial	GTEx
rs7138420	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs7138420	LASS5	cis	parietal	SCAN
rs7138420	LASS5	cis	cerebellum	SCAN
rs7138420	ATF1	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50562000-50584800	Weak transcription	K562	blood
2	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:50564400-50586200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:50570400-50592800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:50570800-50589800	Strong transcription	Fetal Stomach	stomach
8	chr12:50571800-50586000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:50571800-50586200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
12	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:50572000-50586000	Weak transcription	Left Ventricle	heart
15	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
16	chr12:50572600-50586200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:50575600-50586000	Weak transcription	Dnd41	blood
18	chr12:50575800-50585000	Weak transcription	Liver	Liver
19	chr12:50575800-50586000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:50576000-50584600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:50576000-50584600	Weak transcription	Fetal Thymus	thymus
22	chr12:50576000-50586200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:50576600-50595000	Weak transcription	A549	lung
24	chr12:50577800-50583400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:50578600-50586200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:50578800-50583200	Genic enhancers	Fetal Muscle Leg	muscle
27	chr12:50578800-50583400	Genic enhancers	Adipose Nuclei	Adipose
28	chr12:50578800-50583400	Genic enhancers	HMEC	breast
29	chr12:50578800-50585200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:50579000-50583200	Strong transcription	Primary T cells from cord blood	blood
31	chr12:50579000-50583200	Enhancers	Placenta	Placenta
32	chr12:50579000-50583600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:50579200-50584200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:50579600-50583400	Enhancers	Brain Germinal Matrix	brain
35	chr12:50579600-50583400	Genic enhancers	NHLF	lung
36	chr12:50579600-50584600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:50579600-50598000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:50579800-50583600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:50580200-50583600	Enhancers	HepG2	liver
40	chr12:50580400-50583600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:50580400-50595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:50580600-50585200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:50581000-50583200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:50581000-50583200	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr12:50581000-50583200	Genic enhancers	Stomach Smooth Muscle	stomach
46	chr12:50581200-50583400	Genic enhancers	Rectal Mucosa Donor 29	rectum
47	chr12:50581200-50583600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:50581400-50583400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:50581400-50583400	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr12:50581400-50583400	Genic enhancers	HUVEC	blood vessel

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