Variant report

Variant	rs2789498
Chromosome Location	chr6:149775754-149775755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149764839..149766396-chr6:149774052..149775951,2	MCF-7	breast:
2	chr6:149750637..149752761-chr6:149774465..149776310,2	MCF-7	breast:
3	chr6:149769726..149773853-chr6:149775332..149778151,3	K562	blood:

Variant related genes	Relation type
ENSG00000178199	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1001242	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1074495	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1339185	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1934117	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2007062	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2153219	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2744430	0.90[ASN][1000 genomes]
rs2789493	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2789495	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2789496	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2789501	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3765290	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs475681	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897125	0.82[ASN][1000 genomes]
rs512685	0.92[EUR][1000 genomes]
rs556775	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs587155	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62441728	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs632360	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs634440	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs656461	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs664951	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs760897	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs805027	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs909793	0.95[EUR][1000 genomes]
rs9377218	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised 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	3 gene(s)	inside rSNPs	diseases
4	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149768400-149779400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:149769600-149782800	Strong transcription	Primary B cells from peripheral blood	blood
3	chr6:149769600-149787200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:149769800-149779800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:149770000-149779600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:149770000-149785200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:149771600-149778000	Weak transcription	GM12878-XiMat	blood
8	chr6:149771800-149775800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr6:149772000-149788800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:149772200-149776600	Enhancers	Liver	Liver
11	chr6:149772400-149776600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:149772400-149776600	Enhancers	Fetal Lung	lung
13	chr6:149772600-149776400	Enhancers	Small Intestine	intestine
14	chr6:149772600-149779400	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:149772600-149787000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:149772800-149776400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr6:149773000-149776800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:149773000-149778200	Weak transcription	Thymus	Thymus
19	chr6:149773000-149779600	Weak transcription	Primary T cells from cord blood	blood
20	chr6:149773000-149783400	Strong transcription	Primary B cells from cord blood	blood
21	chr6:149773200-149776600	Enhancers	Colonic Mucosa	Colon
22	chr6:149773200-149776600	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:149773400-149777000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:149773600-149778400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:149774000-149775800	Enhancers	Fetal Muscle Trunk	muscle
26	chr6:149774000-149777000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:149774600-149776600	Enhancers	Fetal Muscle Leg	muscle
28	chr6:149774600-149776800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr6:149774600-149777000	Bivalent Enhancer	Fetal Stomach	stomach
30	chr6:149774800-149775800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:149774800-149776000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:149774800-149776000	Enhancers	Aorta	Aorta
33	chr6:149774800-149776000	Enhancers	NHEK	skin
34	chr6:149774800-149776200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:149774800-149776200	Enhancers	Brain Germinal Matrix	brain
36	chr6:149774800-149776200	Enhancers	Fetal Intestine Large	intestine
37	chr6:149774800-149776200	Enhancers	Fetal Thymus	thymus
38	chr6:149774800-149776200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr6:149774800-149776200	Enhancers	HSMM	muscle
40	chr6:149774800-149776400	Enhancers	Ovary	ovary
41	chr6:149774800-149776400	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr6:149774800-149776600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:149774800-149776600	Flanking Active TSS	Hela-S3	cervix
44	chr6:149774800-149776800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:149774800-149776800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:149774800-149776800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:149774800-149776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:149774800-149776800	Enhancers	Placenta	Placenta
49	chr6:149775000-149775800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:149775000-149775800	Enhancers	Monocytes-CD14+_RO01746	blood

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