Variant report

Variant	rs4848978
Chromosome Location	chr2:112816047-112816048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112643670..112645263-chr2:112814283..112816428,2	MCF-7	breast:
2	chr2:112815166..112819031-chr2:112819758..112824247,10	K562	blood:
3	chr2:112767436..112770076-chr2:112815782..112818698,2	K562	blood:
4	chr2:112811708..112814423-chr2:112815526..112819270,5	K562	blood:
5	chr2:112815378..112818291-chr2:112847520..112849051,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153214	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10171979	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10207726	0.80[GIH][hapmap]
rs1113419	0.81[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs11884641	0.81[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap]
rs11884693	0.84[GIH][hapmap];0.82[MEX][hapmap]
rs12469210	0.81[CEU][hapmap]
rs12469847	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12474039	0.81[CEU][hapmap]
rs13015619	0.86[ASN][1000 genomes]
rs1400321	0.84[CEU][hapmap]
rs1400324	0.81[CEU][hapmap]
rs1400325	0.81[CEU][hapmap]
rs17175275	0.81[CEU][hapmap]
rs17175331	0.81[CEU][hapmap]
rs3811632	0.80[GIH][hapmap]
rs3811640	0.82[GIH][hapmap]
rs4078410	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4278932	0.81[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap]
rs4434006	0.81[CEU][hapmap]
rs4491736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528767	0.81[CEU][hapmap]
rs4567941	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4613287	1.00[CHB][hapmap]
rs4848262	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710733	0.81[CEU][hapmap]
rs6712080	0.81[CEU][hapmap]
rs6713344	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6718840	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730521	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs6737707	0.82[CHB][hapmap]
rs6737989	0.81[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs6760032	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563113	0.81[CEU][hapmap]
rs7568632	0.86[JPT][hapmap]
rs7581849	1.00[CHB][hapmap]
rs7595574	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs867311	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs9308665	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308666	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh 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	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1003129	chr2:112691270-112816694	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv1793068	chr2:112784234-112816694	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4848978	IL1RN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112814000-112817400	Enhancers	Small Intestine	intestine
2	chr2:112814200-112816400	Weak transcription	Esophagus	oesophagus
3	chr2:112814200-112816600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:112814200-112817000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr2:112814200-112817000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:112814200-112817200	Enhancers	Stomach Mucosa	stomach
7	chr2:112814200-112821000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:112814200-112827000	Weak transcription	Psoas Muscle	Psoas
9	chr2:112814200-112835400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:112814200-112849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:112814200-112859800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:112814400-112816200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:112814400-112816600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:112814400-112816600	Enhancers	Gastric	stomach
15	chr2:112814400-112816600	Enhancers	Ovary	ovary
16	chr2:112814400-112817400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr2:112814400-112820400	Weak transcription	Aorta	Aorta
18	chr2:112814400-112821400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:112814400-112831600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:112814600-112816400	Enhancers	Right Ventricle	heart
21	chr2:112814600-112816600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:112814600-112816600	Enhancers	Left Ventricle	heart
23	chr2:112814600-112817000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:112814600-112817000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:112814600-112819000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:112814600-112819400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:112814600-112819400	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:112814600-112820600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:112814600-112820600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:112814600-112821600	Weak transcription	Fetal Brain Female	brain
31	chr2:112814600-112829400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:112814800-112816200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:112814800-112816600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:112814800-112816600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:112814800-112816600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:112814800-112816600	Enhancers	K562	blood
37	chr2:112814800-112816800	Weak transcription	Primary T cells from cord blood	blood
38	chr2:112814800-112816800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:112814800-112817000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:112814800-112817000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:112814800-112817000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr2:112814800-112817400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:112814800-112817400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:112814800-112817400	Enhancers	Right Atrium	heart
45	chr2:112814800-112817600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:112814800-112818600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:112814800-112818600	Weak transcription	Liver	Liver
48	chr2:112814800-112818600	Weak transcription	Fetal Kidney	kidney
49	chr2:112814800-112818800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr2:112814800-112819200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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