Variant report

Variant	rs7689226
Chromosome Location	chr4:78792747-78792748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78782527..78785375-chr4:78792236..78798548,6	MCF-7	breast:
2	chr4:78785570..78789084-chr4:78790216..78793354,5	K562	blood:
3	chr4:78791921..78794709-chr4:78802036..78804705,2	MCF-7	breast:
4	chr4:78782878..78784636-chr4:78792721..78794473,2	MCF-7	breast:
5	chr4:78733342..78735297-chr4:78791961..78793861,2	K562	blood:

Variant related genes	Relation type
ENSG00000250214	Chromatin interaction
ENSG00000169288	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10007837	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1010728	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10222901	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1039403	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10428319	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10856982	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10856991	0.81[AMR][1000 genomes]
rs11097900	0.86[AMR][1000 genomes]
rs11097965	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1156059	0.93[AMR][1000 genomes]
rs11721383	0.84[ASN][1000 genomes]
rs11723221	0.90[ASN][1000 genomes]
rs11729703	0.80[ASN][1000 genomes]
rs11730329	0.91[ASN][1000 genomes]
rs11730403	0.91[ASN][1000 genomes]
rs11731374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733759	0.90[ASN][1000 genomes]
rs11737353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11737861	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11939576	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12108312	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12510593	0.84[AMR][1000 genomes]
rs12643960	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13105201	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13118459	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13128914	0.88[AMR][1000 genomes]
rs13131896	0.91[ASN][1000 genomes]
rs13137909	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13144226	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1402626	0.91[ASN][1000 genomes]
rs1521419	0.91[ASN][1000 genomes]
rs1554457	0.91[ASN][1000 genomes]
rs17002823	0.91[ASN][1000 genomes]
rs17002824	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17002825	0.91[ASN][1000 genomes]
rs17002828	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17002829	0.91[ASN][1000 genomes]
rs17002831	0.91[ASN][1000 genomes]
rs1980266	0.91[ASN][1000 genomes]
rs2030463	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2102116	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2134048	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2173869	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2174078	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2174080	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2866688	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2866690	0.88[AMR][1000 genomes]
rs28796999	0.97[ASN][1000 genomes]
rs28891692	0.97[ASN][1000 genomes]
rs3205281	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4078523	0.89[ASN][1000 genomes]
rs4304001	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4365752	0.91[ASN][1000 genomes]
rs4388114	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410552	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4417999	0.80[ASN][1000 genomes]
rs4472161	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4541532	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4546268	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4561950	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4607246	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859872	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55673370	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55694923	0.91[ASN][1000 genomes]
rs55886549	0.91[ASN][1000 genomes]
rs56138517	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57246363	0.91[ASN][1000 genomes]
rs57501818	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57868780	0.99[ASN][1000 genomes]
rs57896992	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58218398	0.96[ASN][1000 genomes]
rs58358199	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60135456	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533217	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6533226	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6533269	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533271	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533274	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6533290	0.91[ASN][1000 genomes]
rs6817305	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6817823	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6821826	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6822317	0.91[ASN][1000 genomes]
rs6823465	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6827822	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6828302	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6829203	0.84[EUR][1000 genomes]
rs6832015	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6833179	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6836627	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6838630	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6839504	0.93[AMR][1000 genomes]
rs6849922	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6850111	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6854989	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72868269	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72869573	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73827437	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73827443	0.91[ASN][1000 genomes]
rs73827451	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7439347	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7656319	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7657658	0.91[ASN][1000 genomes]
rs7659122	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7661064	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7663359	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7671941	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7673642	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7674744	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7675586	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7687170	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7687812	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7692075	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996218	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs7689226	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784400-78793600	Weak transcription	Spleen	Spleen
2	chr4:78784600-78793600	Weak transcription	Left Ventricle	heart
3	chr4:78784600-78795800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:78784600-78801800	Weak transcription	Aorta	Aorta
5	chr4:78784800-78793600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:78784800-78808400	Weak transcription	Brain Substantia Nigra	brain
7	chr4:78784800-78842200	Weak transcription	HSMMtube	muscle
8	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
9	chr4:78785000-78792800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:78785000-78793000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr4:78785000-78793200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:78785000-78793200	Weak transcription	Placenta	Placenta
13	chr4:78785000-78793200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:78785000-78793400	Weak transcription	Brain Germinal Matrix	brain
15	chr4:78785000-78793600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:78785000-78793600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:78785000-78793600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:78785000-78793600	Weak transcription	Gastric	stomach
19	chr4:78785000-78793600	Weak transcription	Lung	lung
20	chr4:78785000-78793600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:78785000-78794400	Weak transcription	Fetal Intestine Small	intestine
22	chr4:78785000-78798400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:78785000-78798800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:78785000-78798800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:78785000-78801400	Weak transcription	Pancreas	Pancrea
26	chr4:78785000-78801400	Weak transcription	Psoas Muscle	Psoas
27	chr4:78785000-78803000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:78785000-78805800	Weak transcription	Colonic Mucosa	Colon
29	chr4:78785000-78807000	Weak transcription	Brain Anterior Caudate	brain
30	chr4:78785000-78808400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:78785000-78808800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:78785000-78810600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:78785000-78831200	Weak transcription	Brain Angular Gyrus	brain
34	chr4:78785000-78831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:78785000-78841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
37	chr4:78785200-78793000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:78785200-78793000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:78785200-78793000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:78785200-78793200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:78785200-78793200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:78785200-78793600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:78785200-78793600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:78785200-78794400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr4:78785200-78794800	Weak transcription	Colon Smooth Muscle	Colon
46	chr4:78785200-78794800	Weak transcription	Fetal Lung	lung
47	chr4:78785200-78798800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:78785200-78805000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:78785200-78806600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:78785200-78808400	Weak transcription	Fetal Brain Male	brain

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