Variant report

Variant	rs1169313
Chromosome Location	chr12:121442670-121442671
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:121441093-121442844	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:121441627-121442718	HepG2	liver:	n/a	n/a
3	CTCF	chr12:121442573-121443738	A549	lung:	n/a	chr12:121443298-121443311
4	ZNF274	chr12:121442592-121442922	NT2-D1	testis:	n/a	n/a
5	POLR2A	chr12:121438511-121442806	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:121441915..121444188-chr12:121446625..121449115,2	K562	blood:
2	chr12:121291153..121292656-chr12:121442284..121444744,2	MCF-7	breast:
3	chr12:121124381..121127314-chr12:121441274..121443258,2	K562	blood:
4	chr12:121437912..121440467-chr12:121441258..121443495,3	MCF-7	breast:
5	chr12:121427353..121429838-chr12:121441548..121443367,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271769	TF binding region
ENSG00000110917	Chromatin interaction
ENSG00000157895	Chromatin interaction
ENSG00000271769	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1169286	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1169300	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1169301	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1169303	0.83[MEX][hapmap]
rs1169306	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169309	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169311	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169314	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1169315	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1182933	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1183910	0.91[YRI][hapmap]
rs2254971	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2257764	0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2257962	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2258043	0.83[MEX][hapmap]
rs2258287	0.86[MEX][hapmap]
rs2259816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2259820	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2259852	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2264750	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2264782	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393791	0.83[GIH][hapmap]
rs2464195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2464196	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[YRI][hapmap];0.96[ASN][1000 genomes]
rs3213545	0.81[CHB][hapmap];0.82[YRI][hapmap]
rs4278584	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7310409	0.83[GIH][hapmap]
rs735396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Liver enzyme levels	18940312	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1169313	C12orf43	cis	parietal	SCAN
rs1169313	FLJ12448	cis	multi-tissue	Pritchard
rs1169313	CABP1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121429800-121451600	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr12:121433200-121448200	Weak transcription	Fetal Kidney	kidney
3	chr12:121436600-121452800	Weak transcription	Fetal Heart	heart
4	chr12:121437400-121442800	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:121437600-121452000	Strong transcription	Fetal Stomach	stomach
6	chr12:121437600-121453000	Weak transcription	Fetal Brain Male	brain
7	chr12:121437600-121453600	Weak transcription	Right Atrium	heart
8	chr12:121437800-121451200	Strong transcription	A549	lung
9	chr12:121438400-121448000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:121438400-121451200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:121438400-121451400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:121438600-121444800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:121438600-121445000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:121438600-121449000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:121438600-121451200	Strong transcription	Spleen	Spleen
16	chr12:121438600-121451400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:121438600-121451400	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:121438600-121451600	Strong transcription	Primary T cells from cord blood	blood
19	chr12:121438600-121451800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:121438800-121443600	Strong transcription	Esophagus	oesophagus
21	chr12:121438800-121444200	Strong transcription	Lung	lung
22	chr12:121438800-121444800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:121438800-121450200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:121438800-121450400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:121438800-121451200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:121438800-121451400	Strong transcription	Fetal Muscle Leg	muscle
27	chr12:121438800-121451600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr12:121438800-121451800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:121438800-121451800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:121438800-121451800	Strong transcription	Fetal Brain Female	brain
31	chr12:121439000-121451200	Strong transcription	Brain Germinal Matrix	brain
32	chr12:121439000-121451400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:121439000-121451600	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr12:121439000-121451800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:121439200-121443800	Strong transcription	Brain Anterior Caudate	brain
36	chr12:121439200-121444200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:121439200-121444400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:121439200-121445200	Weak transcription	K562	blood
39	chr12:121439200-121445600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:121439200-121450400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr12:121439200-121451600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:121439200-121451800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:121439400-121442800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr12:121439400-121443000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:121439400-121450200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:121439400-121451400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:121439400-121451400	Strong transcription	Adipose Nuclei	Adipose
48	chr12:121439400-121451600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:121439400-121451600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:121439400-121451800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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