Variant report

Variant	rs1889733
Chromosome Location	chr6:34359540-34359541
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:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34203144..34206658-chr6:34358641..34361602,5	MCF-7	breast:
2	chr6:34336023..34338003-chr6:34357501..34359863,2	K562	blood:
3	chr19:34662845..34663493-chr6:34359460..34360357,2	Hela-S3	cervix:
4	chr6:34214133..34219385-chr6:34356600..34362053,16	K562	blood:
5	chr6:34202852..34208935-chr6:34358420..34361531,11	K562	blood:
6	chr6:34232571..34234778-chr6:34358274..34360439,2	K562	blood:
7	chr6:34242678..34244532-chr6:34357227..34359923,2	MCF-7	breast:
8	chr6:34202383..34217863-chr6:34357259..34364960,37	K562	blood:
9	chr6:34304154..34306840-chr6:34357586..34359775,2	MCF-7	breast:
10	chr6:34357967..34362826-chr6:34390808..34395314,8	K562	blood:
11	chr6:34213633..34219276-chr6:34358105..34363296,16	MCF-7	breast:
12	chr6:34358195..34361774-chr6:34391620..34393850,4	K562	blood:
13	chr6:34358377..34360251-chr6:34384641..34386602,2	MCF-7	breast:
14	chr6:34358853..34362255-chr6:34392162..34395391,9	MCF-7	breast:
15	chr6:34215295..34220270-chr6:34358417..34361933,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACSIN1-1	chr6:34355460-34360244	NONHSAT112133

No data

Variant related genes	Relation type
ENSG00000257103	Chromatin interaction
ENSG00000137309	Chromatin interaction
ENSG00000186577	Chromatin interaction
ENSG00000270800	Chromatin interaction
ENSG00000124614	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

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]
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]
rs205285	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]
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]
rs2840286	1.00[YRI][hapmap];1.00[AFR][1000 genomes];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]
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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34354000-34359600	Weak transcription	Small Intestine	intestine
2	chr6:34358000-34360800	Active TSS	HMEC	breast
3	chr6:34358000-34361000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:34358000-34361000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:34358000-34361200	Active TSS	NHLF	lung
6	chr6:34358200-34359600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:34358200-34359800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:34358200-34360800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:34358200-34361200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:34358200-34361400	Active TSS	Fetal Brain Female	brain
11	chr6:34358400-34359600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr6:34358400-34359600	Active TSS	Right Atrium	heart
13	chr6:34358400-34359600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr6:34358400-34359800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr6:34358400-34359800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:34358400-34360000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr6:34358400-34360800	Active TSS	Fetal Intestine Small	intestine
18	chr6:34358400-34361000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:34358400-34361000	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:34358400-34361000	Active TSS	A549	lung
21	chr6:34358400-34361200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr6:34358400-34361200	Active TSS	Aorta	Aorta
23	chr6:34358400-34361400	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr6:34358400-34361600	Active TSS	Brain Hippocampus Middle	brain
25	chr6:34358600-34359600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr6:34358600-34359600	Flanking Active TSS	Liver	Liver
27	chr6:34358600-34359600	Flanking Active TSS	Thymus	Thymus
28	chr6:34358600-34359800	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr6:34358600-34359800	Active TSS	Fetal Brain Male	brain
30	chr6:34358600-34360000	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr6:34358600-34360000	Active TSS	Colonic Mucosa	Colon
32	chr6:34358600-34360800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:34358600-34360800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:34358600-34360800	Active TSS	Fetal Muscle Trunk	muscle
35	chr6:34358600-34360800	Active TSS	NHEK	skin
36	chr6:34358600-34361000	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr6:34358600-34361000	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr6:34358600-34361000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:34358600-34361000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:34358600-34361000	Active TSS	Fetal Kidney	kidney
41	chr6:34358600-34361000	Active TSS	Stomach Mucosa	stomach
42	chr6:34358600-34361000	Active TSS	GM12878-XiMat	blood
43	chr6:34358600-34361000	Active TSS	HSMMtube	muscle
44	chr6:34358600-34361200	Active TSS	H1 Cell Line	embryonic stem cell
45	chr6:34358600-34361200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:34358600-34361200	Active TSS	Ovary	ovary
47	chr6:34358600-34361200	Active TSS	Psoas Muscle	Psoas
48	chr6:34358600-34361200	Active TSS	Right Ventricle	heart
49	chr6:34358600-34361200	Active TSS	HSMM	muscle
50	chr6:34358800-34359600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links