Variant report

Variant	rs2066938
Chromosome Location	chr12:121160615-121160616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:121160611-121160960	K562	blood:	n/a	chr12:121160804-121160815
2	EP300	chr12:121159266-121160684	SK-N-SH	brain:	n/a	n/a
3	MYC	chr12:121160527-121160727	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr12:121160589-121160957	Hela-S3	cervix:	n/a	chr12:121160804-121160815
5	CEBPB	chr12:121160544-121160991	IMR90	lung:	n/a	chr12:121160804-121160815

No.	Distal block	Cell Line	Cell type
1	chr12:121123312..121126140-chr12:121158161..121160645,3	K562	blood:
2	chr12:120729375..120731716-chr12:121159185..121161541,3	K562	blood:
3	chr12:121159870..121162504-chr12:121416031..121417915,2	K562	blood:
4	chr12:121157650..121161198-chr12:121163529..121166472,5	K562	blood:

Variant related genes	Relation type
ACADS	TF binding region
MIR4700	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000122971	Chromatin interaction
ENSG00000241388	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000135100	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10431386	0.81[CEU][hapmap]
rs12311479	0.87[ASN][1000 genomes]
rs12828810	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829722	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799958	0.91[EUR][1000 genomes]
rs2014355	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs2239758	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2393778	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3021337	0.93[ASN][1000 genomes]
rs3021338	0.88[ASN][1000 genomes]
rs34030695	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34673751	0.93[EUR][1000 genomes]
rs34708625	0.91[EUR][1000 genomes]
rs34734847	0.97[ASN][1000 genomes]
rs35360964	0.94[ASN][1000 genomes]
rs35525135	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35599677	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35771722	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752531	0.97[ASN][1000 genomes]
rs3916	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3999408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55730005	0.97[ASN][1000 genomes]
rs56273049	0.97[ASN][1000 genomes]
rs57830821	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs60858026	0.93[ASN][1000 genomes]
rs71454661	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7306541	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7313271	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog
Metabolic traits	21886157	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2066938	IL31	cis	cerebellum	SCAN
rs2066938	UNC119B	cis	parietal	SCAN
rs2066938	SPPL3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121149800-121162800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:121150000-121163000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:121150400-121161600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:121150400-121163200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:121150800-121162400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:121150800-121162400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:121151000-121161200	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr12:121151000-121161800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:121151000-121161800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:121151000-121162200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:121151000-121163000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:121151200-121161200	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr12:121151200-121161200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:121151200-121161200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:121151200-121161200	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr12:121151200-121161200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr12:121151200-121161200	Strong transcription	Hela-S3	cervix
18	chr12:121151200-121161200	Strong transcription	HUVEC	blood vessel
19	chr12:121151200-121161400	Strong transcription	Fetal Muscle Leg	muscle
20	chr12:121151200-121161600	Strong transcription	Ovary	ovary
21	chr12:121151200-121161800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:121151200-121162000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:121151200-121162200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:121151200-121162200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:121151200-121162200	Strong transcription	Brain Anterior Caudate	brain
26	chr12:121151200-121162200	Strong transcription	Fetal Thymus	thymus
27	chr12:121151200-121162400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr12:121151200-121162600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:121151200-121162600	Strong transcription	Fetal Stomach	stomach
30	chr12:121151200-121163000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:121151400-121163600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:121151800-121161200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:121151800-121162200	Strong transcription	Left Ventricle	heart
34	chr12:121151800-121162400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:121151800-121162600	Strong transcription	Fetal Lung	lung
36	chr12:121151800-121162600	Strong transcription	Placenta	Placenta
37	chr12:121152000-121161200	Strong transcription	Rectal Smooth Muscle	rectum
38	chr12:121152000-121161600	Strong transcription	Brain Germinal Matrix	brain
39	chr12:121152000-121161600	Strong transcription	Colon Smooth Muscle	Colon
40	chr12:121152200-121161200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:121152200-121161600	Strong transcription	Thymus	Thymus
42	chr12:121152200-121161600	Strong transcription	Dnd41	blood
43	chr12:121152200-121162000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:121152200-121162200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:121152400-121161000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:121152400-121161000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:121152400-121161200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:121152400-121161600	Strong transcription	Primary T cells from cord blood	blood
49	chr12:121152400-121161600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:121152600-121161000	Strong transcription	Placenta Amnion	Placenta Amnion

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