Variant report

Variant	rs13120630
Chromosome Location	chr4:79589102-79589103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79583593..79586061-chr4:79586877..79589613,2	MCF-7	breast:
2	chr4:79588490..79591389-chr4:79613550..79615288,2	K562	blood:
3	chr4:79588830..79590716-chr4:79696797..79699676,2	K562	blood:
4	chr4:79587769..79591719-chr4:79695513..79697602,3	K562	blood:
5	chr4:79575433..79577300-chr4:79588056..79590576,2	MCF-7	breast:
6	chr4:79571552..79573969-chr4:79585909..79589158,3	K562	blood:

Variant related genes	Relation type
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10001246	0.81[CEU][hapmap]
rs10007186	0.90[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10019240	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212636	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1107606	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1108907	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11724268	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724602	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11728013	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731482	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733032	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11733269	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs11736376	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11736602	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233694	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233707	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643488	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12646646	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12650411	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12711032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138005	0.90[CEU][hapmap];0.82[CHB][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1834518	0.86[EUR][1000 genomes]
rs1972024	0.83[EUR][1000 genomes]
rs28597797	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34325799	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4073678	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073679	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074673	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074674	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075927	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077709	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4270605	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306980	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4353930	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4632683	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4643844	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975148	0.85[EUR][1000 genomes]
rs6533821	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs6533825	0.90[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs6533835	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533842	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533845	0.84[AMR][1000 genomes]
rs6533847	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6811335	0.83[EUR][1000 genomes]
rs6811782	0.88[JPT][hapmap]
rs6812227	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814739	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819484	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824014	0.83[EUR][1000 genomes]
rs6829061	0.83[EUR][1000 genomes]
rs6829198	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6834587	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6835210	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835998	0.83[EUR][1000 genomes]
rs6836513	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840592	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841654	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6845893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846346	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6851341	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854055	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6858740	0.88[JPT][hapmap]
rs7317	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs7657082	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs7669674	0.81[AMR][1000 genomes]
rs7669866	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7670506	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7680749	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7680766	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7682984	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7689154	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9998136	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active 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	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13120630	ANXA3	cis	cerebellum	SCAN
rs13120630	PRDM8	cis	parietal	SCAN
rs13120630	CCR1	trans	lymphoblastoid	seeQTL
rs13120630	LOC643424	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79564400-79589600	Weak transcription	Lung	lung
2	chr4:79583800-79593000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr4:79584200-79589200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:79584400-79589200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:79584400-79589200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:79584400-79589200	Weak transcription	NHDF-Ad	bronchial
7	chr4:79585800-79590400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:79586000-79590000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr4:79586000-79590400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:79586000-79590400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:79586000-79590400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:79586800-79590800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr4:79586800-79595400	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:79587200-79590800	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr4:79587400-79589800	Enhancers	HUVEC	blood vessel
16	chr4:79587600-79590000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr4:79587800-79589600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:79587800-79589800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:79587800-79590000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:79587800-79590200	Enhancers	Primary hematopoietic stem cells	blood
21	chr4:79588000-79589400	Enhancers	Primary T cells from cord blood	blood
22	chr4:79588000-79590000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr4:79588000-79590000	Enhancers	Spleen	Spleen
24	chr4:79588000-79590200	Enhancers	Adipose Nuclei	Adipose
25	chr4:79588000-79594400	Enhancers	K562	blood
26	chr4:79588200-79589200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr4:79588200-79589400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr4:79588400-79589400	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr4:79588400-79589800	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:79588400-79591200	Weak transcription	Fetal Intestine Large	intestine
31	chr4:79588400-79593600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:79588600-79589200	Weak transcription	Fetal Intestine Small	intestine
33	chr4:79588600-79589400	Flanking Active TSS	GM12878-XiMat	blood
34	chr4:79588600-79589800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr4:79588800-79589200	Enhancers	Fetal Lung	lung
36	chr4:79588800-79589600	Weak transcription	Placenta	Placenta
37	chr4:79589000-79589200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr4:79589000-79589200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr4:79589000-79589800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:79589000-79590000	Enhancers	Rectal Mucosa Donor 31	rectum

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