Variant report

Variant	rs2677109
Chromosome Location	chr6:45407654-45407655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45342387..45347008-chr6:45403451..45407825,6	K562	blood:
2	chr6:45345002..45348666-chr6:45406844..45410633,4	K562	blood:
3	chr6:45388663..45390976-chr6:45406985..45408759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction
ENSG00000124813	Chromatin interaction
ENSG00000271857	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12197948	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12210100	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1317777	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs1343799	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs1934327	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2256819	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2677099	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2677100	0.92[EUR][1000 genomes]
rs2677110	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2790093	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2790094	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs2790095	0.96[EUR][1000 genomes]
rs2790097	0.95[EUR][1000 genomes]
rs2790098	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2790099	0.95[EUR][1000 genomes]
rs2790100	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs2790102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790103	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2819852	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2819853	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2819861	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2819864	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2819865	0.86[EUR][1000 genomes]
rs2819866	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2819867	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2820339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2820340	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs4711816	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6458443	0.90[CEU][hapmap];0.99[EUR][1000 genomes]
rs6905689	0.83[JPT][hapmap]
rs765724	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs7751050	0.83[JPT][hapmap]
rs7756144	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9885645	0.91[CEU][hapmap];0.95[EUR][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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45394400-45413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:45399800-45410600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:45400200-45409600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:45402000-45413200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:45403000-45410600	Enhancers	Fetal Thymus	thymus
7	chr6:45403400-45408400	Enhancers	K562	blood
8	chr6:45403800-45407800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:45403800-45413200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:45404000-45408000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:45405000-45407800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:45405000-45407800	Enhancers	NHEK	skin
13	chr6:45405000-45408000	Enhancers	HMEC	breast
14	chr6:45405000-45413000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:45405000-45413200	Weak transcription	Brain Anterior Caudate	brain
16	chr6:45405200-45407800	Genic enhancers	HSMM	muscle
17	chr6:45405200-45408000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:45405200-45417200	Weak transcription	Spleen	Spleen
19	chr6:45405400-45413400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:45405600-45407800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:45405600-45411600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:45405600-45412200	Weak transcription	Primary B cells from cord blood	blood
23	chr6:45405600-45412400	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:45405600-45413200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:45405600-45413200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:45405600-45413400	Weak transcription	Brain Angular Gyrus	brain
27	chr6:45405600-45413800	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:45405600-45417400	Genic enhancers	Dnd41	blood
29	chr6:45405800-45407800	Enhancers	NHLF	lung
30	chr6:45405800-45409400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:45406000-45407800	Genic enhancers	NH-A	brain
32	chr6:45406200-45407800	Genic enhancers	NHDF-Ad	bronchial
33	chr6:45406400-45407800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr6:45406400-45412000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:45406600-45407800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr6:45406600-45407800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr6:45406600-45407800	Enhancers	Thymus	Thymus
38	chr6:45406600-45412200	Weak transcription	Fetal Intestine Small	intestine
39	chr6:45406800-45407800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:45407000-45407800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr6:45407000-45407800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:45407000-45407800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:45407000-45408000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:45407000-45413200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:45407000-45413400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:45407200-45407800	Genic enhancers	Muscle Satellite Cultured Cells	--
47	chr6:45407200-45407800	Genic enhancers	Osteobl	bone
48	chr6:45407200-45408000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:45407200-45413000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:45407200-45413000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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