Variant report

Variant	rs10005935
Chromosome Location	chr4:78682581-78682582
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10005531	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap]
rs10007837	0.82[YRI][hapmap]
rs10019920	0.81[CHB][hapmap]
rs10026176	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap]
rs10222901	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs11737861	0.80[LWK][hapmap]
rs11931686	0.94[ASW][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap]
rs12509847	0.88[ASW][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap]
rs12510593	0.86[YRI][hapmap]
rs1587563	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17002804	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1809919	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996740	0.87[GIH][hapmap];0.80[MEX][hapmap]
rs2102116	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs2134048	0.80[LWK][hapmap]
rs2173869	0.82[YRI][hapmap]
rs2866688	0.83[YRI][hapmap]
rs2866690	0.82[YRI][hapmap]
rs3205281	0.80[LWK][hapmap]
rs4128860	0.89[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs4304001	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs4388114	0.83[YRI][hapmap]
rs4410552	0.80[LWK][hapmap];0.89[YRI][hapmap]
rs4859512	0.81[CHB][hapmap]
rs4859513	0.81[CHB][hapmap]
rs4859882	0.85[CHB][hapmap]
rs4859884	0.85[CHB][hapmap]
rs6533225	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811439	0.81[ASN][1000 genomes]
rs6816134	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6825492	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835993	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839504	0.83[YRI][hapmap]
rs6849145	0.92[CHD][hapmap];0.81[GIH][hapmap]
rs6850111	0.82[YRI][hapmap]
rs7682450	0.80[CHB][hapmap];0.93[YRI][hapmap]
rs7687812	0.83[YRI][hapmap]
rs7698009	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs924684	0.81[CHB][hapmap];0.81[LWK][hapmap]
rs9654194	1.00[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10005935	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs10005935	G3BP2	cis	parietal	SCAN
rs10005935	BTC	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

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	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
6	chr4:78650200-78697800	Weak transcription	Gastric	stomach
7	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
10	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
12	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
13	chr4:78659800-78685800	Weak transcription	Psoas Muscle	Psoas
14	chr4:78659800-78697800	Weak transcription	Esophagus	oesophagus
15	chr4:78662000-78695600	Weak transcription	Ovary	ovary
16	chr4:78662000-78697600	Weak transcription	Brain Angular Gyrus	brain
17	chr4:78662000-78697800	Weak transcription	Pancreas	Pancrea
18	chr4:78662200-78697800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:78662800-78683400	Weak transcription	Fetal Kidney	kidney
20	chr4:78662800-78683600	Weak transcription	K562	blood
21	chr4:78663800-78695600	Weak transcription	Left Ventricle	heart
22	chr4:78667200-78682600	Weak transcription	HepG2	liver
23	chr4:78673400-78682600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:78673400-78687000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:78673400-78692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:78676200-78683400	Weak transcription	GM12878-XiMat	blood
27	chr4:78676200-78687400	Strong transcription	Fetal Thymus	thymus
28	chr4:78677400-78682800	Strong transcription	Dnd41	blood
29	chr4:78677800-78682600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr4:78677800-78693800	Weak transcription	Hela-S3	cervix
31	chr4:78677800-78698400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:78678000-78691200	Weak transcription	Placenta	Placenta
33	chr4:78678000-78691800	Weak transcription	HUVEC	blood vessel
34	chr4:78678000-78692400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:78678000-78698400	Weak transcription	HSMM	muscle
36	chr4:78678200-78682600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:78678400-78692600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:78679200-78683600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:78679400-78682600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:78679400-78684000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:78679600-78686600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:78680200-78683800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:78681200-78682800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr4:78681200-78692800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr4:78681400-78682600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:78681600-78682600	Strong transcription	Fetal Lung	lung
47	chr4:78681600-78684000	ZNF genes & repeats	Fetal Brain Female	brain
48	chr4:78681600-78692200	Weak transcription	Fetal Stomach	stomach
49	chr4:78681800-78683600	ZNF genes & repeats	Fetal Muscle Leg	muscle
50	chr4:78682000-78684200	ZNF genes & repeats	Primary T cells from cord blood	blood

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