Variant report

Variant	rs2840286
Chromosome Location	chr6:34355766-34355767
allele	C/T
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:7)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34353371..34356590-chr6:34358788..34361729,3	MCF-7	breast:
2	chr6:34355515..34358143-chr6:34358689..34360982,3	MCF-7	breast:
3	chr6:34329241..34330151-chr6:34355752..34356539,2	K562	blood:
4	chr6:34355541..34358575-chr6:34361768..34363900,3	K562	blood:
5	chr6:34344409..34346828-chr6:34354344..34357154,2	K562	blood:
6	chr6:34349500..34351699-chr6:34352826..34355839,3	K562	blood:
7	chr6:34216778..34218402-chr6:34353840..34355861,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACSIN1-1	chr6:34355460-34360244	NONHSAT112133
2	lnc-PACSIN1-1	chr6:34355417-34357076	l_3174_chr6:34355416-34362546_76bGuttman_hLF
3	lnc-RPS10-1	chr6:34355435-34357947	ucscGeneNc_uc003ojj_2

No data

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction
ENSG00000186577	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10947509	1.00[AMR][1000 genomes]
rs12660150	1.00[AFR][1000 genomes]
rs172280	1.00[YRI][hapmap]
rs182280	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1889733	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs205271	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs205272	1.00[AMR][1000 genomes]
rs205273	1.00[AMR][1000 genomes]
rs205274	1.00[AMR][1000 genomes]
rs205275	1.00[AMR][1000 genomes]
rs205277	1.00[AMR][1000 genomes]
rs205278	1.00[AMR][1000 genomes]
rs206922	1.00[YRI][hapmap]
rs206928	1.00[YRI][hapmap]
rs206929	1.00[AMR][1000 genomes]
rs206931	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs206932	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs206933	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs206934	1.00[AMR][1000 genomes]
rs206938	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs206939	1.00[AMR][1000 genomes]
rs206940	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2182382	1.00[AMR][1000 genomes]
rs2274347	1.00[JPT][hapmap]
rs2395557	1.00[AMR][1000 genomes]
rs2395558	1.00[AMR][1000 genomes]
rs2395563	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2395565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2395566	1.00[AMR][1000 genomes]
rs2894399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3843524	1.00[AMR][1000 genomes]
rs3846865	1.00[AMR][1000 genomes]
rs3846870	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3857561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs443351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs453919	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs460389	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs462194	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs466031	1.00[YRI][hapmap]
rs4713778	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4713814	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6457780	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6457782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6457783	1.00[AMR][1000 genomes]
rs6908420	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6913723	1.00[AMR][1000 genomes]
rs6918865	1.00[AMR][1000 genomes]
rs6922059	1.00[AMR][1000 genomes]
rs7760590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7764155	1.00[CHD][hapmap]
rs7773372	1.00[YRI][hapmap]
rs7774674	1.00[AMR][1000 genomes]
rs9296118	1.00[AMR][1000 genomes]
rs9394233	1.00[YRI][hapmap]
rs9461986	1.00[AFR][1000 genomes];1.00[AMR][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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1034978	chr6:34327526-34362187	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv981324	chr6:34351435-34360764	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34318200-34355800	Weak transcription	Brain Germinal Matrix	brain
2	chr6:34327800-34356400	Weak transcription	Hela-S3	cervix
3	chr6:34328600-34358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:34331000-34358400	Weak transcription	Aorta	Aorta
5	chr6:34333600-34358000	Weak transcription	HMEC	breast
6	chr6:34335600-34358800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:34337800-34359000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:34338200-34358600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:34338400-34356600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:34339200-34358000	Weak transcription	NHEK	skin
11	chr6:34339400-34358000	Weak transcription	HUVEC	blood vessel
12	chr6:34340400-34358000	Weak transcription	Fetal Thymus	thymus
13	chr6:34342600-34355800	Weak transcription	Fetal Brain Female	brain
14	chr6:34343000-34357600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:34343400-34356600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:34345200-34358600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:34346600-34358400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:34346800-34356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:34349000-34358800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:34350600-34359000	Weak transcription	Esophagus	oesophagus
21	chr6:34351400-34358000	Weak transcription	Placenta	Placenta
22	chr6:34351600-34357400	Enhancers	Psoas Muscle	Psoas
23	chr6:34351600-34358000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:34351600-34358200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:34351800-34357000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:34351800-34358000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr6:34352000-34355800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:34352000-34356800	Weak transcription	Gastric	stomach
29	chr6:34352000-34356800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:34352000-34357200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:34352000-34358000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:34352000-34358000	Weak transcription	NH-A	brain
33	chr6:34352000-34358600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:34352000-34358800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:34352200-34355800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:34352200-34357200	Enhancers	HepG2	liver
37	chr6:34352200-34358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:34352200-34358000	Weak transcription	Fetal Stomach	stomach
39	chr6:34352200-34358800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:34352400-34358000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:34352400-34358000	Weak transcription	HSMM	muscle
42	chr6:34352400-34358400	Weak transcription	Fetal Lung	lung
43	chr6:34352400-34358400	Weak transcription	HSMMtube	muscle
44	chr6:34352400-34358600	Weak transcription	Primary T cells from cord blood	blood
45	chr6:34352600-34355800	Weak transcription	Fetal Kidney	kidney
46	chr6:34352600-34358400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:34352600-34358600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:34352800-34355800	Weak transcription	Adipose Nuclei	Adipose
49	chr6:34352800-34356600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:34352800-34357000	Weak transcription	Primary B cells from cord blood	blood

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