Variant report

Variant	rs1516629
Chromosome Location	chr2:112658779-112658780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112658476..112659217-chr2:112777886..112778574,2	MCF-7	breast:
2	chr2:112640266..112649080-chr2:112649576..112660203,14	MCF-7	breast:
3	chr2:112657825..112659209-chr2:112806011..112807065,8	MCF-7	breast:
4	chr2:112651539..112654934-chr2:112657187..112660968,3	K562	blood:
5	chr2:112658215..112658830-chr2:112806155..112807049,3	K562	blood:

Variant related genes	Relation type
ENSG00000236307	Chromatin interaction
ENSG00000153107	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

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];0.89[EUR][1000 genomes]
rs11884641	0.95[CEU][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11884693	0.90[CEU][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11887652	0.83[EUR][1000 genomes]
rs11893308	0.81[EUR][1000 genomes]
rs11902247	0.89[EUR][1000 genomes]
rs12466812	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469210	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs12470338	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12474039	0.95[CEU][hapmap]
rs12477716	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]
rs1400321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1400324	0.95[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1400325	0.95[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][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];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17175275	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs17175331	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs17835605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001201	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2001444	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.83[EUR][1000 genomes]
rs4349353	0.83[EUR][1000 genomes]
rs4434006	0.95[CEU][hapmap];0.93[YRI][hapmap];0.88[EUR][1000 genomes]
rs4521048	0.82[EUR][1000 genomes]
rs4528767	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs55708724	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55728465	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55766181	0.83[EUR][1000 genomes]
rs55785997	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55792453	0.81[EUR][1000 genomes]
rs55799805	0.83[EUR][1000 genomes]
rs55972521	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56272510	0.89[EUR][1000 genomes]
rs57640566	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57732600	0.82[EUR][1000 genomes]
rs58065683	0.83[EUR][1000 genomes]
rs58641606	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59650987	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61583444	0.82[EUR][1000 genomes]
rs6710733	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6712080	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6713344	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs6729037	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730521	0.95[CEU][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs6737989	0.95[CEU][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7563113	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7568632	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7575552	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7578057	0.89[EUR][1000 genomes]
rs867311	0.95[CEU][hapmap];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv961869	chr2:112645626-112660962	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1516629	IL1RN	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112655200-112659400	Active TSS	Right Atrium	heart
2	chr2:112655400-112658800	Active TSS	Aorta	Aorta
3	chr2:112655600-112658800	Active TSS	Brain Substantia Nigra	brain
4	chr2:112655600-112658800	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr2:112655600-112659000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:112655600-112659000	Active TSS	Brain Cingulate Gyrus	brain
7	chr2:112655600-112659000	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr2:112655600-112659200	Active TSS	Stomach Smooth Muscle	stomach
9	chr2:112657000-112662600	Weak transcription	Spleen	Spleen
10	chr2:112657000-112663400	Weak transcription	Dnd41	blood
11	chr2:112657000-112663600	Weak transcription	Small Intestine	intestine
12	chr2:112657200-112658800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:112657400-112658800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:112657400-112659000	Flanking Active TSS	HepG2	liver
15	chr2:112657400-112659000	Flanking Active TSS	HUVEC	blood vessel
16	chr2:112657400-112660600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:112657400-112661200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:112657400-112661600	Weak transcription	Right Ventricle	heart
19	chr2:112657400-112662200	Weak transcription	Gastric	stomach
20	chr2:112657400-112662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:112657400-112664400	Weak transcription	Pancreas	Pancrea
22	chr2:112657600-112658800	Enhancers	Primary hematopoietic stem cells	blood
23	chr2:112657600-112659000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:112657600-112660000	Weak transcription	Left Ventricle	heart
25	chr2:112657800-112658800	Enhancers	Adipose Nuclei	Adipose
26	chr2:112657800-112658800	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr2:112657800-112659000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:112657800-112659000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:112657800-112661000	Weak transcription	Fetal Kidney	kidney
30	chr2:112657800-112662200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:112657800-112662400	Weak transcription	Brain Angular Gyrus	brain
32	chr2:112658000-112659000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:112658000-112659000	Active TSS	Duodenum Mucosa	Duodenum
34	chr2:112658000-112660000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:112658000-112662400	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:112658200-112658800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:112658200-112658800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:112658200-112658800	Flanking Active TSS	Liver	Liver
39	chr2:112658200-112658800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr2:112658200-112659000	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:112658200-112659000	Enhancers	Fetal Intestine Large	intestine
42	chr2:112658200-112659000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
43	chr2:112658200-112659200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr2:112658400-112658800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr2:112658400-112658800	Enhancers	Lung	lung
46	chr2:112658400-112658800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr2:112658400-112658800	Enhancers	K562	blood
48	chr2:112658400-112659000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:112658400-112659000	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr2:112658400-112660600	Weak transcription	Fetal Intestine Small	intestine

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