Variant report

Variant	rs9993942
Chromosome Location	chr4:78649236-78649237
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78647944..78650924-chr4:78655794..78657335,2	MCF-7	breast:
2	chr4:78648017..78651931-chr4:78652126..78656070,5	K562	blood:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10005741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10007837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10222901	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1039403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1039467	0.91[AMR][1000 genomes]
rs10428319	0.92[CHB][hapmap]
rs10856982	0.88[ASN][1000 genomes]
rs11097935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11097965	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs1156059	0.84[ASN][1000 genomes]
rs11721383	0.87[CEU][hapmap];0.92[CHB][hapmap];0.87[AMR][1000 genomes]
rs11723029	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11723221	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes]
rs11727993	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11729703	0.87[AMR][1000 genomes]
rs11730329	0.94[AMR][1000 genomes]
rs11730403	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11731374	1.00[CHB][hapmap]
rs11732039	0.87[CEU][hapmap];0.92[CHB][hapmap];0.91[AMR][1000 genomes]
rs11733759	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11734428	0.91[AMR][1000 genomes]
rs11737353	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs11737861	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12510593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12643960	1.00[ASN][1000 genomes]
rs13105201	0.96[ASN][1000 genomes]
rs13111592	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13118459	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13128914	0.96[ASN][1000 genomes]
rs13131896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13137909	0.88[ASN][1000 genomes]
rs13138341	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13144225	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13144226	0.88[ASN][1000 genomes]
rs1402626	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1501373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1521419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1553386	0.91[AMR][1000 genomes]
rs1554457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17002823	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17002825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002831	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1813725	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1814033	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1847216	0.91[AMR][1000 genomes]
rs1980266	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2030463	0.90[ASN][1000 genomes]
rs2062637	0.92[JPT][hapmap]
rs2102116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2134048	0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs2134459	0.91[AMR][1000 genomes]
rs2173869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2866444	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2866688	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2866689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2866690	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs28796999	0.90[AMR][1000 genomes]
rs28891692	0.90[AMR][1000 genomes]
rs2903291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3205281	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4078523	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4304001	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4331798	0.85[AMR][1000 genomes]
rs4365752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4388114	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs4410552	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4417999	0.87[AMR][1000 genomes]
rs4472161	0.94[ASN][1000 genomes]
rs4473672	0.85[AMR][1000 genomes]
rs4541532	0.88[ASN][1000 genomes]
rs4561950	0.92[CHB][hapmap];0.87[CHD][hapmap]
rs4859506	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859872	0.95[ASN][1000 genomes]
rs4859876	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55694923	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55886549	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57221952	0.91[AMR][1000 genomes]
rs57246363	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57868780	0.87[AMR][1000 genomes]
rs58054752	0.91[AMR][1000 genomes]
rs58218398	0.90[AMR][1000 genomes]
rs6533217	0.95[ASN][1000 genomes]
rs6533226	1.00[ASN][1000 genomes]
rs6533239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533269	0.88[ASN][1000 genomes]
rs6533270	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533271	0.88[ASN][1000 genomes]
rs6533272	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533274	0.85[ASN][1000 genomes]
rs6533290	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs6533358	0.87[AMR][1000 genomes]
rs6533359	0.91[AMR][1000 genomes]
rs6814830	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6817305	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6817823	0.88[ASN][1000 genomes]
rs6821826	0.92[CHB][hapmap]
rs6822317	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6823465	0.93[ASN][1000 genomes]
rs6827822	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6828302	0.84[ASN][1000 genomes]
rs6830993	0.85[AMR][1000 genomes]
rs6833179	0.95[ASN][1000 genomes]
rs6839504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6849922	0.85[ASN][1000 genomes]
rs6850049	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6850111	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6850590	0.91[AMR][1000 genomes]
rs6855336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6857067	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73827443	0.84[AMR][1000 genomes]
rs73827456	0.85[AMR][1000 genomes]
rs73827459	0.91[AMR][1000 genomes]
rs73827460	0.91[AMR][1000 genomes]
rs7439347	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs7655949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7657658	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7661064	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs7663359	0.92[CHB][hapmap]
rs7669988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671941	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs7674744	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7687170	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs7687812	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs7693256	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs885376	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9991424	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9993942	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78629000-78649400	Weak transcription	HMEC	breast
2	chr4:78629200-78676600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:78629400-78649400	Weak transcription	Spleen	Spleen
4	chr4:78629400-78656200	Weak transcription	Small Intestine	intestine
5	chr4:78630200-78660000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:78631200-78656000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:78631600-78649400	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:78631600-78652600	Weak transcription	Esophagus	oesophagus
9	chr4:78631800-78649400	Weak transcription	Aorta	Aorta
10	chr4:78632000-78651800	Weak transcription	HepG2	liver
11	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
12	chr4:78635600-78652800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr4:78636000-78651600	Weak transcription	Fetal Heart	heart
14	chr4:78636200-78649600	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:78636400-78659000	Weak transcription	Psoas Muscle	Psoas
16	chr4:78636800-78649400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:78636800-78655400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr4:78637200-78649400	Weak transcription	NHDF-Ad	bronchial
19	chr4:78637400-78649400	Weak transcription	Ovary	ovary
20	chr4:78637400-78661200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:78637400-78673200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:78637600-78649400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:78638800-78652200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:78638800-78655200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr4:78639200-78649400	Weak transcription	HUVEC	blood vessel
26	chr4:78639200-78661200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:78639400-78649400	Weak transcription	Fetal Brain Female	brain
28	chr4:78639400-78650400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:78639400-78671200	Weak transcription	Brain Germinal Matrix	brain
30	chr4:78639600-78652800	Weak transcription	NHEK	skin
31	chr4:78639800-78649400	Weak transcription	Right Ventricle	heart
32	chr4:78640000-78649400	Weak transcription	Brain Anterior Caudate	brain
33	chr4:78640000-78653000	Weak transcription	GM12878-XiMat	blood
34	chr4:78640200-78652800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:78640200-78652800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:78640200-78656200	Strong transcription	Fetal Thymus	thymus
37	chr4:78640400-78649800	Weak transcription	Osteobl	bone
38	chr4:78640400-78653600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:78640400-78654400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:78640400-78654400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:78640400-78655800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:78640600-78650800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:78640600-78651000	Strong transcription	Adipose Nuclei	Adipose
44	chr4:78640600-78652200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:78640600-78653000	Strong transcription	Liver	Liver
46	chr4:78640600-78654400	Strong transcription	Dnd41	blood
47	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
48	chr4:78641000-78665000	Weak transcription	Fetal Brain Male	brain
49	chr4:78641800-78650600	Strong transcription	Primary T cells from cord blood	blood
50	chr4:78641800-78653200	Strong transcription	Primary B cells from cord blood	blood

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