Variant report

Variant	rs3094114
Chromosome Location	chr6:30738921-30738922
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30649121..30651445-chr6:30738828..30742388,3	K562	blood:
2	chr6:30735343..30739242-chr6:30745410..30750382,5	MCF-7	breast:
3	chr10:104401695..104404644-chr6:30737594..30739724,2	MCF-7	breast:
4	chr6:30736125..30739794-chr6:30850488..30852740,4	MCF-7	breast:
5	chr6:30639159..30640838-chr6:30736824..30738928,2	MCF-7	breast:
6	chr6:30736036..30738964-chr6:30760194..30762277,2	K562	blood:
7	chr6:30735347..30739906-chr6:30783605..30789456,10	MCF-7	breast:
8	chr6:30583226..30586077-chr6:30737832..30742122,4	K562	blood:
9	chr6:30735402..30739247-chr6:30785239..30791444,10	MCF-7	breast:
10	chr6:30726903..30729816-chr6:30736090..30739671,3	K562	blood:
11	chr6:30293972..30296069-chr6:30738821..30740521,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204599	Chromatin interaction
ENSG00000171206	Chromatin interaction
ENSG00000272933	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000204568	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs3094115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094117	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3095339	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3131036	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132601	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4248148	0.93[ASN][1000 genomes]
rs6906722	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6911571	0.98[ASN][1000 genomes]
rs6911628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912077	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9262184	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9262185	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3094114	NKAPL	cis	cerebellum	SCAN
rs3094114	HIST1H2AM	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30726800-30739000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:30734800-30747400	Weak transcription	Liver	Liver
3	chr6:30735400-30739000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:30735400-30739200	Enhancers	Thymus	Thymus
5	chr6:30736400-30739000	Enhancers	NHDF-Ad	bronchial
6	chr6:30737000-30739000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:30737400-30739000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr6:30737400-30739000	Enhancers	HMEC	breast
9	chr6:30737400-30739400	Enhancers	Primary T cells from cord blood	blood
10	chr6:30737600-30739000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:30737600-30739000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:30737600-30739000	Enhancers	K562	blood
13	chr6:30737600-30742400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:30737600-30742400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:30737600-30742400	Weak transcription	Left Ventricle	heart
16	chr6:30737600-30744200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:30737600-30746000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:30737600-30746000	Weak transcription	Fetal Lung	lung
19	chr6:30737600-30746000	Weak transcription	Gastric	stomach
20	chr6:30737600-30746000	Weak transcription	Lung	lung
21	chr6:30737600-30746000	Weak transcription	Pancreas	Pancrea
22	chr6:30737600-30746000	Weak transcription	Right Atrium	heart
23	chr6:30737600-30746000	Weak transcription	Right Ventricle	heart
24	chr6:30737600-30746000	Weak transcription	Spleen	Spleen
25	chr6:30737600-30746200	Weak transcription	Psoas Muscle	Psoas
26	chr6:30737600-30746600	Weak transcription	Aorta	Aorta
27	chr6:30737600-30749200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:30737800-30739000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:30738000-30739000	Enhancers	HSMMtube	muscle
30	chr6:30738000-30739000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr6:30738000-30739000	Enhancers	NHEK	skin
32	chr6:30738000-30739200	Enhancers	HepG2	liver
33	chr6:30738000-30741600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:30738000-30741800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:30738000-30742400	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:30738000-30742400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:30738000-30746000	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:30738000-30746400	Weak transcription	Esophagus	oesophagus
39	chr6:30738200-30739000	Enhancers	A549	lung
40	chr6:30738200-30739200	Enhancers	Hela-S3	cervix
41	chr6:30738200-30741600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:30738200-30741800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:30738200-30742000	Weak transcription	Fetal Heart	heart
44	chr6:30738200-30742000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr6:30738200-30742400	Weak transcription	Placenta	Placenta
46	chr6:30738200-30742600	Weak transcription	HSMM	muscle
47	chr6:30738200-30745200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr6:30738400-30739200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:30738400-30740400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr6:30738400-30747000	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links