Variant report

Variant	rs6533225
Chromosome Location	chr4:78642389-78642390
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78642128..78644545-chr4:78649464..78651620,2	MCF-7	breast:
2	chr4:78641368..78643849-chr4:78739049..78741787,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10005531	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[YRI][hapmap]
rs10005935	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10026176	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap]
rs11931686	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs12509847	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1587563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17002804	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1809919	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4128860	0.80[CEU][hapmap];0.89[YRI][hapmap]
rs4642272	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4859512	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs4859882	0.81[CEU][hapmap];0.90[CHB][hapmap];0.97[YRI][hapmap]
rs4859884	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs4859890	0.81[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap]
rs6816134	0.85[ASN][1000 genomes]
rs6825492	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6835993	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7682450	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs7698009	0.80[AFR][1000 genomes]
rs9654194	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6533225	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78621400-78645800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:78621600-78643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:78626400-78644400	Weak transcription	Placenta	Placenta
4	chr4:78626400-78645200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:78628400-78648400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:78629000-78649400	Weak transcription	HMEC	breast
7	chr4:78629200-78676600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:78629400-78649400	Weak transcription	Spleen	Spleen
9	chr4:78629400-78656200	Weak transcription	Small Intestine	intestine
10	chr4:78630000-78643600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:78630200-78660000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:78631200-78656000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:78631400-78643400	Weak transcription	Gastric	stomach
14	chr4:78631600-78649400	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:78631600-78652600	Weak transcription	Esophagus	oesophagus
16	chr4:78631800-78649400	Weak transcription	Aorta	Aorta
17	chr4:78632000-78651800	Weak transcription	HepG2	liver
18	chr4:78632400-78642800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
20	chr4:78633600-78642800	Weak transcription	Fetal Stomach	stomach
21	chr4:78633600-78645200	Weak transcription	Pancreas	Pancrea
22	chr4:78634000-78647600	Weak transcription	HSMM	muscle
23	chr4:78634200-78643400	Weak transcription	Lung	lung
24	chr4:78634400-78643400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:78634600-78642400	Weak transcription	HSMMtube	muscle
26	chr4:78634800-78643000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:78634800-78643000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:78635000-78646000	Weak transcription	Fetal Lung	lung
29	chr4:78635600-78652800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr4:78636000-78651600	Weak transcription	Fetal Heart	heart
31	chr4:78636200-78646000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:78636200-78647400	Weak transcription	Fetal Kidney	kidney
33	chr4:78636200-78649600	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:78636400-78659000	Weak transcription	Psoas Muscle	Psoas
35	chr4:78636600-78645000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:78636800-78649400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:78636800-78655400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr4:78637200-78647400	Weak transcription	K562	blood
39	chr4:78637200-78649400	Weak transcription	NHDF-Ad	bronchial
40	chr4:78637400-78649400	Weak transcription	Ovary	ovary
41	chr4:78637400-78661200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:78637400-78673200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:78637600-78649400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:78638000-78642600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr4:78638000-78644800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:78638600-78642400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:78638800-78652200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:78638800-78655200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:78639000-78643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:78639200-78643000	Weak transcription	Fetal Muscle Leg	muscle

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