Variant report

Variant	rs1587563
Chromosome Location	chr4:78734563-78734564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78727559..78729935-chr4:78732783..78735387,2	MCF-7	breast:
2	chr4:78721732..78724295-chr4:78733166..78737485,4	K562	blood:
3	chr4:78733342..78735297-chr4:78791961..78793861,2	K562	blood:
4	chr4:78727738..78737799-chr4:78737984..78742271,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10005531	0.85[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap]
rs10005935	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]
rs10007837	0.82[YRI][hapmap]
rs10018117	0.87[ASN][1000 genomes]
rs10019920	0.85[CHB][hapmap]
rs10026176	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[ASN][1000 genomes]
rs10027634	0.82[ASN][1000 genomes]
rs10222901	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs11737861	0.80[LWK][hapmap]
rs11931686	0.94[ASW][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11942975	0.82[ASN][1000 genomes]
rs12509847	0.88[ASW][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12510593	0.86[YRI][hapmap]
rs13131331	0.82[ASN][1000 genomes]
rs17002804	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1809919	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1996740	0.85[GIH][hapmap]
rs2102116	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs2134048	0.80[LWK][hapmap]
rs2173869	0.82[YRI][hapmap]
rs28436599	0.84[ASN][1000 genomes]
rs2866688	0.83[YRI][hapmap]
rs2866690	0.82[YRI][hapmap]
rs28685099	0.86[ASN][1000 genomes]
rs3205281	0.80[LWK][hapmap]
rs4128860	0.92[CHD][hapmap];0.80[GIH][hapmap]
rs4304001	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs4328941	0.82[ASN][1000 genomes]
rs4388114	0.83[YRI][hapmap]
rs4410552	0.80[LWK][hapmap];0.89[YRI][hapmap]
rs4859512	0.85[CHB][hapmap]
rs4859513	0.85[CHB][hapmap]
rs4859882	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs4859884	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs6533225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs67814821	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6811439	0.92[ASN][1000 genomes]
rs6816134	0.99[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6825492	0.92[ASN][1000 genomes]
rs6835993	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6839504	0.83[YRI][hapmap]
rs6849145	0.94[CHD][hapmap];0.82[ASN][1000 genomes]
rs6850111	0.82[YRI][hapmap]
rs7660788	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7682450	0.85[CHB][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs7687812	0.83[YRI][hapmap]
rs7698009	0.85[ASN][1000 genomes]
rs924684	0.85[CHB][hapmap];0.81[LWK][hapmap]
rs9654194	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9994366	0.81[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	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
3	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1587563	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs1587563	CCDC158	cis	parietal	SCAN
rs1587563	G3BP2	cis	parietal	SCAN
rs1587563	BTC	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78718800-78738600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:78720800-78735600	Weak transcription	HepG2	liver
3	chr4:78722200-78738600	Weak transcription	HSMM	muscle
4	chr4:78722400-78734800	Weak transcription	Fetal Intestine Large	intestine
5	chr4:78722600-78735800	Weak transcription	A549	lung
6	chr4:78722600-78737800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:78722600-78737800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:78722600-78738600	Weak transcription	NHEK	skin
9	chr4:78722600-78739000	Weak transcription	Ovary	ovary
10	chr4:78722600-78739200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:78722800-78736800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:78722800-78738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:78723000-78734800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:78723000-78738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:78723200-78738600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:78724000-78735000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:78724000-78736000	Weak transcription	HUVEC	blood vessel
18	chr4:78724000-78736800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:78724400-78735600	Weak transcription	Liver	Liver
20	chr4:78724400-78738600	Weak transcription	Colonic Mucosa	Colon
21	chr4:78724800-78738600	Weak transcription	Brain Substantia Nigra	brain
22	chr4:78725600-78734800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:78725800-78736800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr4:78725800-78738600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr4:78727200-78737800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr4:78727400-78735600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:78727400-78735800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:78727400-78735800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:78728600-78738600	Weak transcription	Psoas Muscle	Psoas
30	chr4:78728800-78736600	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:78728800-78738600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:78729000-78736600	Weak transcription	Colon Smooth Muscle	Colon
33	chr4:78730400-78738600	Weak transcription	K562	blood
34	chr4:78732200-78735400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr4:78732200-78736200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr4:78732200-78736400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:78732200-78736400	Weak transcription	Brain Anterior Caudate	brain
38	chr4:78732200-78736600	Weak transcription	Aorta	Aorta
39	chr4:78732200-78738600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:78732400-78738600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:78732800-78734800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:78732800-78735200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:78732800-78735800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:78732800-78738800	Weak transcription	Lung	lung
45	chr4:78733200-78734800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:78733200-78734800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:78733200-78736600	Weak transcription	Small Intestine	intestine
48	chr4:78733200-78738600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:78733400-78734800	Enhancers	Primary T cells from cord blood	blood
50	chr4:78733400-78735200	Enhancers	Primary T helper cells PMA-I stimulated	--

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