Variant report

Variant	rs12477716
Chromosome Location	chr2:112668644-112668645
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	chr2:112655484..112657101-chr2:112668303..112670079,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153208	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10207726	0.89[CHD][hapmap]
rs1113419	0.95[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs11884641	0.95[CEU][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11884693	0.90[CEU][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11887652	0.85[EUR][1000 genomes]
rs11893308	0.82[EUR][1000 genomes]
rs11902247	0.90[EUR][1000 genomes]
rs12466812	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12469210	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12470338	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12474039	0.95[CEU][hapmap]
rs1400321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400324	0.95[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1400325	0.95[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1516629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17174870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17175275	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs17175331	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs17835605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001201	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2001444	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3811632	0.89[CHD][hapmap]
rs4278932	0.95[CEU][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4349353	0.85[EUR][1000 genomes]
rs4434006	0.95[CEU][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes]
rs4521048	0.83[EUR][1000 genomes]
rs4528767	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs55708724	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55728465	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55766181	0.85[EUR][1000 genomes]
rs55785997	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55792453	0.82[EUR][1000 genomes]
rs55799805	0.85[EUR][1000 genomes]
rs55972521	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56272510	0.91[EUR][1000 genomes]
rs57640566	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57732600	0.83[EUR][1000 genomes]
rs58065683	0.84[EUR][1000 genomes]
rs58641606	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59650987	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61583444	0.83[EUR][1000 genomes]
rs6710733	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs6712080	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6713344	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs6729037	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6730521	0.95[CEU][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6737989	0.95[CEU][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs7563113	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7568632	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7575552	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578057	0.91[EUR][1000 genomes]
rs867311	0.95[CEU][hapmap];0.98[EUR][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	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases
5	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv998028	chr2:112649472-112734015	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv582701	chr2:112649472-112740597	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv526647	chr2:112651316-112738562	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv582702	chr2:112651316-112738562	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12477716	IL1RN	cis	parietal	SCAN
rs12477716	MERTK	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112660200-112674400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:112662800-112675800	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:112662800-112677000	Weak transcription	Spleen	Spleen
4	chr2:112663000-112677800	Weak transcription	Right Ventricle	heart
5	chr2:112664200-112669000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:112664200-112669000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:112664600-112674400	Weak transcription	Fetal Stomach	stomach
8	chr2:112664600-112675800	Weak transcription	HUVEC	blood vessel
9	chr2:112664600-112676000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:112664600-112676600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:112664600-112687600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:112664600-112702200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:112664800-112670200	Weak transcription	Placenta	Placenta
14	chr2:112664800-112670200	Weak transcription	Right Atrium	heart
15	chr2:112664800-112674600	Weak transcription	Lung	lung
16	chr2:112664800-112675600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:112664800-112676200	Weak transcription	Thymus	Thymus
18	chr2:112664800-112676600	Weak transcription	Pancreas	Pancrea
19	chr2:112665800-112669400	Weak transcription	Left Ventricle	heart
20	chr2:112666400-112680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:112666400-112681800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:112666400-112692800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:112666600-112680800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:112666800-112670200	Enhancers	HepG2	liver
25	chr2:112666800-112675600	Weak transcription	K562	blood
26	chr2:112666800-112677400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:112667000-112669000	Enhancers	Brain Hippocampus Middle	brain
28	chr2:112667000-112674600	Weak transcription	Gastric	stomach
29	chr2:112667000-112682000	Weak transcription	Aorta	Aorta
30	chr2:112667000-112684400	Weak transcription	Brain Angular Gyrus	brain
31	chr2:112667200-112670200	Weak transcription	Ovary	ovary
32	chr2:112667200-112674400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:112667200-112675800	Weak transcription	Fetal Intestine Large	intestine
34	chr2:112667400-112676000	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:112667600-112668800	Enhancers	Duodenum Mucosa	Duodenum
36	chr2:112667800-112682000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:112668000-112668800	Enhancers	Fetal Kidney	kidney
38	chr2:112668200-112668800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:112668200-112668800	Enhancers	Brain Cingulate Gyrus	brain
40	chr2:112668200-112668800	Enhancers	Fetal Lung	lung
41	chr2:112668200-112669000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:112668200-112674400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:112668400-112668800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr2:112668400-112668800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:112668400-112668800	Enhancers	Adipose Nuclei	Adipose
46	chr2:112668400-112668800	Flanking Active TSS	Liver	Liver
47	chr2:112668400-112668800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:112668400-112668800	Enhancers	Brain Substantia Nigra	brain
49	chr2:112668400-112668800	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr2:112668400-112668800	Enhancers	Rectal Mucosa Donor 31	rectum

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