Variant report

Variant	rs10049674
Chromosome Location	chr4:78843512-78843513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78836963..78838899-chr4:78841325..78844073,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10005531	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10018117	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10019920	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10026176	0.96[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10027634	0.83[EUR][1000 genomes]
rs10027739	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10030568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1010728	0.83[YRI][hapmap]
rs1106457	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11931471	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11931686	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11942975	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12108312	0.83[YRI][hapmap]
rs12509847	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13131331	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13131974	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1393643	0.82[ASN][1000 genomes]
rs1604609	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2036455	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs2036457	0.92[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2088995	0.82[ASN][1000 genomes]
rs2102192	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28417234	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28436599	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28483318	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28685099	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4128860	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4328941	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4561950	0.89[YRI][hapmap]
rs4859512	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859513	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859882	0.92[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4859884	0.92[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4859890	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533355	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533372	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs67814821	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6814088	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6820725	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6849145	0.88[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7436080	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7439347	0.89[YRI][hapmap]
rs7659122	0.83[YRI][hapmap]
rs7660788	0.81[EUR][1000 genomes]
rs7663359	0.83[YRI][hapmap]
rs7682450	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7687170	0.89[YRI][hapmap]
rs873280	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs924684	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs924685	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9654194	0.82[CHD][hapmap]
rs9985806	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9994366	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10049674	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
2	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
3	chr4:78794000-78851200	Weak transcription	Spleen	Spleen
4	chr4:78794200-78851800	Weak transcription	Lung	lung
5	chr4:78802400-78858400	Weak transcription	Aorta	Aorta
6	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
8	chr4:78808800-78852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:78809200-78847000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:78809600-78851200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:78809600-78851400	Weak transcription	Ovary	ovary
12	chr4:78809600-78865400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:78810000-78851800	Weak transcription	Thymus	Thymus
15	chr4:78814600-78874400	Weak transcription	Pancreas	Pancrea
16	chr4:78816400-78866400	Weak transcription	Fetal Thymus	thymus
17	chr4:78816400-78876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:78816600-78851400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:78816600-78875800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:78818800-78872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:78819200-78846200	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:78819200-78852000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:78819600-78851200	Weak transcription	Adipose Nuclei	Adipose
24	chr4:78820800-78851200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr4:78821000-78849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:78821000-78866000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:78821400-78873200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:78830000-78866600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:78830200-78846400	Weak transcription	Fetal Intestine Small	intestine
30	chr4:78830200-78847200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:78830200-78851200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:78830200-78852000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:78830400-78877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:78831800-78865800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:78832000-78845600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:78832000-78846800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:78832000-78851400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:78832000-78858000	Weak transcription	Fetal Stomach	stomach
39	chr4:78833400-78845200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:78833400-78845600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:78833400-78846600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr4:78833400-78847200	Weak transcription	K562	blood
43	chr4:78833400-78851400	Weak transcription	Liver	Liver
44	chr4:78833600-78865400	Weak transcription	Fetal Kidney	kidney
45	chr4:78833800-78845600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:78834000-78852800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:78834800-78845600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr4:78834800-78845600	Weak transcription	Dnd41	blood
49	chr4:78834800-78847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:78835200-78845600	Weak transcription	Monocytes-CD14+_RO01746	blood

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