Variant report

Variant	rs2799080
Chromosome Location	chr6:28265311-28265312
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28262644..28265417-chr6:28284862..28286533,2	MCF-7	breast:
2	chr6:28263544..28266110-chr6:28280477..28282083,2	K562	blood:
3	chr6:28264442..28268560-chr6:28269964..28273646,5	K562	blood:
4	chr6:28264981..28267059-chr6:28281908..28283935,2	MCF-7	breast:
5	chr6:28252167..28254655-chr6:28264060..28265912,2	MCF-7	breast:
6	chr6:28264732..28267471-chr6:28301531..28305480,4	K562	blood:
7	chr6:28265276..28267226-chr6:28297300..28300691,3	MCF-7	breast:
8	chr6:28264329..28266427-chr6:28269486..28272144,3	K562	blood:
9	chr6:28255421..28258446-chr6:28262353..28265432,3	K562	blood:
10	chr6:28265086..28267081-chr6:28267676..28269860,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1144707	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1150667	1.00[AMR][1000 genomes]
rs1150675	1.00[AMR][1000 genomes]
rs1150677	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1150681	1.00[AMR][1000 genomes]
rs1150706	1.00[AMR][1000 genomes]
rs12208060	1.00[AMR][1000 genomes]
rs1225589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225601	1.00[AMR][1000 genomes]
rs1233663	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1233668	1.00[AMR][1000 genomes]
rs1778485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs213229	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs213234	1.00[AMR][1000 genomes]
rs213242	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2394048	1.00[AMR][1000 genomes]
rs2531829	1.00[AMR][1000 genomes]
rs2743874	1.00[YRI][hapmap]
rs2859357	1.00[YRI][hapmap]
rs2859361	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2859366	1.00[AMR][1000 genomes]
rs4713154	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs59183152	1.00[AMR][1000 genomes]
rs6902266	1.00[AMR][1000 genomes]
rs853675	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs853677	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs853680	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs853686	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs853691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs853692	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28250000-28293800	Weak transcription	Gastric	stomach
4	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
5	chr6:28250400-28265600	Weak transcription	Primary T cells from cord blood	blood
6	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:28250600-28267000	Weak transcription	NHEK	skin
8	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
9	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
11	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
13	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:28255200-28268600	Weak transcription	Ovary	ovary
17	chr6:28255200-28271200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:28255200-28271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
20	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
21	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
23	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:28255400-28271200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:28255400-28278400	Weak transcription	HepG2	liver
26	chr6:28255600-28271400	Weak transcription	Placenta	Placenta
27	chr6:28255600-28272000	Weak transcription	Brain Substantia Nigra	brain
28	chr6:28256000-28267600	Weak transcription	Osteobl	bone
29	chr6:28256400-28268400	Weak transcription	Fetal Intestine Large	intestine
30	chr6:28256400-28271600	Weak transcription	Liver	Liver
31	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:28256600-28268200	Weak transcription	Lung	lung
33	chr6:28256600-28268600	Weak transcription	Fetal Thymus	thymus
34	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:28257600-28268000	Weak transcription	K562	blood
36	chr6:28257600-28268400	Weak transcription	Right Ventricle	heart
37	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
38	chr6:28257800-28268600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:28257800-28279000	Weak transcription	HMEC	breast
40	chr6:28258000-28268200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:28258000-28268600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:28258000-28268800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:28258000-28270800	Weak transcription	NH-A	brain
44	chr6:28258200-28268000	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:28258200-28268600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:28258400-28268400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:28258400-28269600	Weak transcription	Fetal Kidney	kidney
48	chr6:28258400-28273800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:28258600-28268600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:28258600-28273000	Weak transcription	Fetal Brain Male	brain

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