Variant report

Variant	rs560218
Chromosome Location	chr6:33552444-33552445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33550386..33552584-chr6:33755194..33756833,2	MCF-7	breast:
2	chr6:33551460..33554975-chr6:33588078..33592105,4	K562	blood:
3	chr6:33546298..33549471-chr6:33550091..33553469,5	K562	blood:
4	chr6:33550022..33555745-chr6:33586647..33590467,5	MCF-7	breast:
5	chr6:33551901..33555908-chr6:33676752..33679381,5	K562	blood:
6	chr6:33552057..33555351-chr6:33600748..33604007,3	MCF-7	breast:
7	chr6:33547287..33549306-chr6:33551969..33553577,2	K562	blood:
8	chr6:33551917..33554088-chr6:33585146..33588477,3	K562	blood:
9	chr6:33384739..33386700-chr6:33551719..33554109,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000096433	Chromatin interaction
ENSG00000030110	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12529825	1.00[JPT][hapmap]
rs1536042	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16869178	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1705000	1.00[ASN][1000 genomes]
rs1755041	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755042	1.00[ASN][1000 genomes]
rs1755054	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627049	1.00[YRI][hapmap]
rs1794686	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794688	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068236	1.00[ASN][1000 genomes]
rs2147655	1.00[ASN][1000 genomes]
rs2395451	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4711333	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4711334	1.00[ASN][1000 genomes]
rs4713642	1.00[MEX][hapmap]
rs4713647	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4713652	1.00[ASN][1000 genomes]
rs472990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480568	1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485623	0.82[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525623	1.00[CHD][hapmap]
rs535584	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542056	1.00[ASN][1000 genomes]
rs542725	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549719	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55700437	1.00[ASN][1000 genomes]
rs557559	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559290	1.00[CHD][hapmap]
rs561276	1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572708	1.00[CHD][hapmap]
rs572824	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59572422	1.00[ASN][1000 genomes]
rs61687548	1.00[ASN][1000 genomes]
rs649775	1.00[CHD][hapmap]
rs653536	1.00[CHD][hapmap]
rs6900438	1.00[ASN][1000 genomes]
rs6906810	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928341	1.00[ASN][1000 genomes]
rs71536195	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752930	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7757391	1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs7757722	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs7759154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762843	1.00[JPT][hapmap]
rs7769019	1.00[MEX][hapmap]
rs7775313	1.00[ASN][1000 genomes]
rs791900	1.00[CHD][hapmap]
rs806604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806605	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9368770	1.00[ASN][1000 genomes]
rs9689326	1.00[EUR][1000 genomes];1.00[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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33548200-33553000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr6:33548200-33553000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:33548400-33552600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:33548400-33552600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:33548400-33552600	Weak transcription	GM12878-XiMat	blood
6	chr6:33548400-33552800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:33548400-33552800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:33548400-33553000	Weak transcription	Primary B cells from cord blood	blood
9	chr6:33548400-33553000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:33548400-33553000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:33548400-33553000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:33548400-33553000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:33548400-33553000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:33548400-33553000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:33548400-33553000	Weak transcription	Thymus	Thymus
16	chr6:33548400-33553000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:33548400-33553200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:33548400-33553200	Weak transcription	Brain Angular Gyrus	brain
19	chr6:33548400-33553200	Weak transcription	HMEC	breast
20	chr6:33548400-33553400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:33548400-33553400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:33548400-33553400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:33548400-33553400	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:33548400-33553400	Weak transcription	Brain Substantia Nigra	brain
25	chr6:33548400-33553400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:33548400-33553400	Weak transcription	Fetal Brain Male	brain
27	chr6:33548400-33553400	Weak transcription	Fetal Heart	heart
28	chr6:33548400-33553400	Weak transcription	Fetal Lung	lung
29	chr6:33548400-33553400	Weak transcription	Placenta	Placenta
30	chr6:33548400-33553400	Weak transcription	HSMMtube	muscle
31	chr6:33548400-33553400	Weak transcription	HUVEC	blood vessel
32	chr6:33548400-33553400	Weak transcription	NH-A	brain
33	chr6:33548400-33553600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:33548400-33553600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:33548400-33553600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:33548400-33553600	Weak transcription	Brain Germinal Matrix	brain
37	chr6:33548400-33553600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:33548400-33553600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:33548400-33553600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:33548400-33557000	Weak transcription	HSMM	muscle
41	chr6:33548400-33557200	Weak transcription	NHDF-Ad	bronchial
42	chr6:33548400-33557600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:33548400-33557800	Weak transcription	Right Atrium	heart
44	chr6:33548600-33552600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:33548600-33552600	Weak transcription	Primary T cells from cord blood	blood
46	chr6:33548600-33552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:33548600-33552800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:33548600-33552800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:33548600-33553000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:33548600-33553000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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