Variant report

Variant	rs3980846
Chromosome Location	chr18:29712504-29712505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29703390..29707950-chr18:29711661..29715023,4	K562	blood:
2	chr18:29703952..29707950-chr18:29710554..29715618,4	K562	blood:

Variant related genes	Relation type
ENSG00000134758	Chromatin interaction
ENSG00000263393	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10048285	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10048287	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1054667	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853418	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10853419	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11081746	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11081747	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11661197	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11663563	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12458837	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12458851	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12604223	0.81[AMR][1000 genomes]
rs12605137	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1808891	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2010813	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2018380	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2048245	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3980848	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4799632	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4799633	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7238559	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8092272	0.80[ASN][1000 genomes]
rs9676102	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs993897	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3980846	RNF138	cis	multi-tissue	Pritchard
rs3980846	RNF138	Cis_1M	lymphoblastoid	RTeQTL
rs3980846	RNF138	cis	Esophagus Mucosa	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29673400-29713800	Weak transcription	Spleen	Spleen
2	chr18:29673800-29714000	Weak transcription	Esophagus	oesophagus
3	chr18:29673800-29714200	Weak transcription	Ovary	ovary
4	chr18:29673800-29715200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:29673800-29715200	Weak transcription	Lung	lung
6	chr18:29673800-29715800	Weak transcription	Colonic Mucosa	Colon
7	chr18:29673800-29717000	Weak transcription	HSMMtube	muscle
8	chr18:29675000-29717200	Weak transcription	NH-A	brain
9	chr18:29676800-29717200	Weak transcription	Brain Germinal Matrix	brain
10	chr18:29677000-29713800	Weak transcription	Small Intestine	intestine
11	chr18:29677000-29715600	Weak transcription	Fetal Heart	heart
12	chr18:29677000-29717000	Weak transcription	Aorta	Aorta
13	chr18:29687200-29713600	Strong transcription	Dnd41	blood
14	chr18:29689400-29713600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr18:29689800-29713200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr18:29691000-29712600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr18:29691200-29713600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr18:29691400-29715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr18:29691600-29713000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr18:29695200-29713200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr18:29695800-29715200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:29695800-29717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr18:29697000-29714200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr18:29699600-29715400	Weak transcription	Left Ventricle	heart
25	chr18:29702200-29712600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr18:29702200-29713600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr18:29704000-29713600	Strong transcription	Primary B cells from cord blood	blood
28	chr18:29704200-29714600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr18:29705400-29713800	Weak transcription	Brain Anterior Caudate	brain
30	chr18:29705400-29714000	Weak transcription	Brain Hippocampus Middle	brain
31	chr18:29705400-29714200	Weak transcription	HUVEC	blood vessel
32	chr18:29705400-29715400	Weak transcription	Fetal Kidney	kidney
33	chr18:29705400-29716400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr18:29705400-29717800	Weak transcription	A549	lung
35	chr18:29705600-29713800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr18:29705800-29713400	Weak transcription	Psoas Muscle	Psoas
37	chr18:29705800-29713400	Weak transcription	Thymus	Thymus
38	chr18:29705800-29713600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr18:29705800-29715200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr18:29706000-29713000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr18:29706000-29713400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr18:29706200-29715200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr18:29706200-29715600	Weak transcription	Fetal Muscle Leg	muscle
44	chr18:29706200-29718600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr18:29706800-29713800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr18:29707200-29715200	Weak transcription	Fetal Lung	lung
47	chr18:29707400-29718400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr18:29707800-29717200	Weak transcription	HSMM	muscle
49	chr18:29708000-29715000	Weak transcription	Placenta	Placenta
50	chr18:29708600-29713000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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