Variant report

Variant	rs4859509
Chromosome Location	chr4:78793258-78793259
allele	A/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
ENSG00000169288	Chromatin interaction
ENSG00000250214	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10033527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033613	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097938	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11729215	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12645742	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13101418	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13101987	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13103035	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13103523	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13104947	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13106067	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13119606	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13120272	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16996915	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17002849	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2088992	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2134050	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28404443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28855210	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34830788	0.85[ASN][1000 genomes]
rs35648590	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35735677	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35979107	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4453957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4571357	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577601	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859511	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859877	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4859879	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4859888	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859889	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62302728	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62302732	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6533282	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6533344	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6533345	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66825464	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6811736	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6814912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6848029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6854895	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7670157	0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675009	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7676660	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7698627	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs905376	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4859509	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs4859509	MRPL1	cis	multi-tissue	Pritchard

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	chr4:78785000-78793400	Weak transcription	Brain Germinal Matrix	brain
10	chr4:78785000-78793600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:78785000-78793600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:78785000-78793600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:78785000-78793600	Weak transcription	Gastric	stomach
14	chr4:78785000-78793600	Weak transcription	Lung	lung
15	chr4:78785000-78793600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:78785000-78794400	Weak transcription	Fetal Intestine Small	intestine
17	chr4:78785000-78798400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:78785000-78798800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:78785000-78798800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:78785000-78801400	Weak transcription	Pancreas	Pancrea
21	chr4:78785000-78801400	Weak transcription	Psoas Muscle	Psoas
22	chr4:78785000-78803000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:78785000-78805800	Weak transcription	Colonic Mucosa	Colon
24	chr4:78785000-78807000	Weak transcription	Brain Anterior Caudate	brain
25	chr4:78785000-78808400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:78785000-78808800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:78785000-78810600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:78785000-78831200	Weak transcription	Brain Angular Gyrus	brain
29	chr4:78785000-78831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:78785000-78841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
32	chr4:78785200-78793600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:78785200-78793600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:78785200-78794400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:78785200-78794800	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:78785200-78794800	Weak transcription	Fetal Lung	lung
37	chr4:78785200-78798800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:78785200-78805000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:78785200-78806600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:78785200-78808400	Weak transcription	Fetal Brain Male	brain
41	chr4:78785200-78816200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:78785200-78818800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:78785200-78820800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr4:78785400-78795200	Weak transcription	NHDF-Ad	bronchial
45	chr4:78785400-78797000	Weak transcription	Thymus	Thymus
46	chr4:78785400-78798800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:78785400-78808200	Weak transcription	Fetal Kidney	kidney
48	chr4:78785400-78829800	Weak transcription	Fetal Heart	heart
49	chr4:78785600-78793800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:78785600-78793800	Weak transcription	Rectal Mucosa Donor 29	rectum

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