Variant report

Variant	rs4859877
Chromosome Location	chr4:78695138-78695139
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	chr4:78676527..78678706-chr4:78694641..78697046,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10033527	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10033613	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11097938	0.82[ASW][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728886	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729215	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12645742	0.85[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13101418	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs13101987	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103035	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13103523	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13104947	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13106067	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13119606	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13120272	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16996915	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2134050	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28404443	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34830788	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35735677	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4453957	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4577601	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs4859509	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4859511	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4859875	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859879	0.82[ASW][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859888	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4859889	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap]
rs6533282	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6533291	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6533344	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6814912	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6848029	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6854895	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7670157	0.82[ASW][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[MKK][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7675009	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]
rs7676660	0.81[ASN][1000 genomes]
rs7698627	0.91[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv518757	chr4:78637265-78695138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4859877	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
2	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
3	chr4:78643800-78714000	Weak transcription	Lung	lung
4	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:78650200-78697800	Weak transcription	Gastric	stomach
6	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
9	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
11	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
12	chr4:78659800-78697800	Weak transcription	Esophagus	oesophagus
13	chr4:78662000-78695600	Weak transcription	Ovary	ovary
14	chr4:78662000-78697600	Weak transcription	Brain Angular Gyrus	brain
15	chr4:78662000-78697800	Weak transcription	Pancreas	Pancrea
16	chr4:78662200-78697800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:78663800-78695600	Weak transcription	Left Ventricle	heart
18	chr4:78677800-78698400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:78678000-78698400	Weak transcription	HSMM	muscle
20	chr4:78682800-78697200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:78683600-78698400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:78684000-78695600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:78684000-78695600	Weak transcription	HepG2	liver
24	chr4:78684000-78697400	Weak transcription	GM12878-XiMat	blood
25	chr4:78684000-78697600	Weak transcription	Brain Anterior Caudate	brain
26	chr4:78684000-78697800	Weak transcription	Fetal Brain Female	brain
27	chr4:78684000-78697800	Weak transcription	Fetal Kidney	kidney
28	chr4:78684000-78697800	Weak transcription	HMEC	breast
29	chr4:78684000-78697800	Weak transcription	K562	blood
30	chr4:78684000-78697800	Weak transcription	NHDF-Ad	bronchial
31	chr4:78684200-78695400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:78684200-78695600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:78684400-78697600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:78685600-78698000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:78686000-78698000	Weak transcription	NHEK	skin
36	chr4:78686600-78698000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:78687200-78697800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:78687200-78697800	Weak transcription	Psoas Muscle	Psoas
39	chr4:78687600-78697400	Weak transcription	Fetal Heart	heart
40	chr4:78687800-78697800	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:78688400-78697600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:78688400-78698000	Strong transcription	Primary B cells from cord blood	blood
43	chr4:78688400-78698000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:78689200-78698000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr4:78689800-78695800	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:78689800-78696400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:78689800-78698000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:78689800-78698400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr4:78690000-78696400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:78690000-78697200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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