Variant report

Variant	rs7675009
Chromosome Location	chr4:78743401-78743402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78738764..78744926-chr4:78780904..78785516,9	MCF-7	breast:
2	chr4:78714906..78717368-chr4:78741847..78743752,2	K562	blood:
3	chr4:78734703..78743448-chr4:78779372..78785561,20	K562	blood:
4	chr4:78738995..78744410-chr4:78782336..78785612,12	K562	blood:
5	chr4:78664695..78666373-chr4:78741463..78744231,2	K562	blood:
6	chr4:78741277..78744126-chr4:78747638..78749332,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10033527	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10033613	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097938	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.96[ASN][1000 genomes]
rs11728886	0.84[ASN][1000 genomes]
rs11729215	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12645742	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13101418	0.81[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap]
rs13101987	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs13103035	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13103523	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13104947	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs13106067	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13119606	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13120272	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.91[ASN][1000 genomes]
rs16996915	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.92[ASN][1000 genomes]
rs2088992	0.89[JPT][hapmap]
rs2134050	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28404443	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28855210	0.87[ASN][1000 genomes]
rs34830788	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs35735677	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4453957	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4571357	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4577601	0.84[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs4859509	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859511	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859875	0.84[ASN][1000 genomes]
rs4859877	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs4859879	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.94[ASN][1000 genomes]
rs4859888	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859889	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6533282	0.83[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533291	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533344	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs6814912	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs6848029	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6854895	0.84[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs7670157	0.82[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7676660	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7698627	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905376	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7675009	C4orf26	cis	parietal	SCAN
rs7675009	MRPL1	cis	cerebellum	SCAN
rs7675009	FRAS1	cis	parietal	SCAN
rs7675009	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs7675009	MRPL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78742000-78743600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr4:78742000-78743800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr4:78742200-78744000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr4:78742400-78744000	Enhancers	Fetal Muscle Leg	muscle
5	chr4:78742400-78744400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr4:78742600-78743600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr4:78742600-78743600	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr4:78742800-78743800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:78742800-78744600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:78742800-78744600	Enhancers	Duodenum Mucosa	Duodenum
11	chr4:78742800-78744600	Enhancers	Fetal Thymus	thymus
12	chr4:78742800-78744800	Enhancers	Primary B cells from peripheral blood	blood
13	chr4:78742800-78745000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:78742800-78745000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr4:78742800-78747200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:78743000-78743600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:78743000-78745400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:78743200-78744800	Enhancers	Primary B cells from cord blood	blood
19	chr4:78743200-78745000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:78743200-78750000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr4:78743400-78743600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:78743400-78743800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr4:78743400-78743800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:78743400-78743800	Enhancers	Placenta	Placenta
25	chr4:78743400-78743800	Enhancers	Dnd41	blood
26	chr4:78743400-78744200	Enhancers	Primary hematopoietic stem cells	blood
27	chr4:78743400-78744400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:78743400-78744600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr4:78743400-78744600	Enhancers	Thymus	Thymus
30	chr4:78743400-78745600	Enhancers	Primary T cells from cord blood	blood
31	chr4:78743400-78745600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr4:78743400-78749800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:78743400-78750200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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