Variant report

Variant	rs2064097
Chromosome Location	chr6:15476619-15476620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15475822..15477498-chr6:15521346..15524316,2	K562	blood:
2	chr6:15244530..15246061-chr6:15474801..15476749,2	K562	blood:
3	chr6:15469193..15474455-chr6:15475135..15479397,6	K562	blood:
4	chr6:15474184..15476635-chr6:15488076..15490844,2	K562	blood:
5	chr6:15473996..15477838-chr6:15479843..15483274,5	K562	blood:
6	chr6:15474412..15476958-chr6:15485865..15488051,2	MCF-7	breast:
7	chr6:15474274..15478303-chr6:15480821..15484291,4	K562	blood:

Variant related genes	Relation type
ENSG00000271888	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1546851	1.00[ASN][1000 genomes]
rs2049950	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2049951	1.00[ASN][1000 genomes]
rs2049952	1.00[ASN][1000 genomes]
rs2064098	0.98[ASN][1000 genomes]
rs2064100	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2179167	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2237111	0.93[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs2237112	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237114	0.93[ASN][1000 genomes]
rs2237115	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2237122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2237125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2237126	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2237127	0.94[CHB][hapmap];1.00[ASN][1000 genomes]
rs2237128	1.00[ASN][1000 genomes]
rs2237129	1.00[ASN][1000 genomes]
rs2237130	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2237131	1.00[ASN][1000 genomes]
rs2237134	0.95[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2237135	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2237136	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2237137	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2251828	1.00[ASN][1000 genomes]
rs2282818	0.93[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2282822	1.00[ASN][1000 genomes]
rs2282824	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2299038	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299040	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299041	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299042	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35720984	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3819398	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712252	0.98[ASN][1000 genomes]
rs4715976	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6912499	1.00[ASN][1000 genomes]
rs6929454	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs727734	1.00[ASN][1000 genomes]
rs760660	0.90[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926309	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370814	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9383058	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9396587	0.90[AMR][1000 genomes];0.96[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	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15435800-15487600	Weak transcription	Colonic Mucosa	Colon
2	chr6:15444600-15477400	Weak transcription	Hela-S3	cervix
3	chr6:15446600-15479800	Weak transcription	Gastric	stomach
4	chr6:15448200-15479800	Weak transcription	Pancreas	Pancrea
5	chr6:15453000-15481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:15457000-15480800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:15458400-15484200	Weak transcription	Small Intestine	intestine
8	chr6:15460800-15480000	Weak transcription	Stomach Mucosa	stomach
9	chr6:15461600-15491000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:15463000-15479800	Weak transcription	Fetal Brain Male	brain
11	chr6:15463800-15479800	Weak transcription	Brain Germinal Matrix	brain
12	chr6:15464800-15479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:15465600-15480000	Weak transcription	Fetal Brain Female	brain
14	chr6:15468400-15478200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:15468600-15476800	Strong transcription	Primary T cells from cord blood	blood
16	chr6:15468800-15476800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr6:15468800-15477600	Strong transcription	HepG2	liver
18	chr6:15468800-15478400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:15469400-15480400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:15469600-15481200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:15470000-15478800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:15470000-15480000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:15470200-15481600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:15471000-15488200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:15471000-15502000	Weak transcription	A549	lung
26	chr6:15471400-15481000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:15471400-15488200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:15471800-15480000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr6:15472000-15484200	Weak transcription	Liver	Liver
30	chr6:15472600-15478000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:15472800-15477200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:15473200-15476800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:15473200-15476800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:15473200-15478400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:15474000-15477800	Genic enhancers	Fetal Thymus	thymus
36	chr6:15474000-15478400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
37	chr6:15474000-15478400	Enhancers	NHLF	lung
38	chr6:15474200-15478400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:15474400-15477000	Weak transcription	Brain Substantia Nigra	brain
40	chr6:15474400-15480600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:15474600-15477200	Weak transcription	NHEK	skin
42	chr6:15474600-15477400	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr6:15474600-15480000	Weak transcription	HSMMtube	muscle
44	chr6:15474800-15477000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:15474800-15477400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:15474800-15479800	Weak transcription	HSMM	muscle
47	chr6:15475000-15476800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:15475000-15477600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:15475000-15478200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
50	chr6:15475200-15476800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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