Variant report

Variant	rs2299054
Chromosome Location	chr6:15398849-15398850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr6:15398809-15399284	GM12878	blood:	n/a	n/a
2	NFIC	chr6:15398752-15399433	GM12878	blood:	n/a	n/a
3	ATF2	chr6:15398786-15399336	GM12878	blood:	n/a	n/a
4	MXI1	chr6:15398733-15399192	GM12878	blood:	n/a	n/a
5	WRNIP1	chr6:15398781-15399221	GM12878	blood:	n/a	n/a
6	RUNX3	chr6:15398723-15399401	GM12878	blood:	n/a	n/a
7	MTA3	chr6:15398758-15399578	GM12878	blood:	n/a	n/a
8	CHD2	chr6:15398802-15399216	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:15368801..15370843-chr6:15397622..15400552,2	K562	blood:
2	chr6:15374975..15376583-chr6:15397138..15400134,2	MCF-7	breast:
3	chr6:15397861..15400160-chr6:15471488..15473543,2	K562	blood:
4	chr6:15211244..15213237-chr6:15398595..15400625,2	K562	blood:
5	chr6:15245364..15247878-chr6:15398194..15399991,2	K562	blood:

No data

Variant related genes	Relation type
JARID2	TF binding region
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1474588	0.84[CEU][hapmap]
rs2072819	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2076055	0.80[CEU][hapmap]
rs2237121	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs2237124	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2237141	0.86[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs2237145	0.84[CEU][hapmap]
rs2237149	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2237150	0.96[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2237152	0.84[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2237153	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2237154	0.91[CHB][hapmap]
rs2237155	0.91[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2237156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237157	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2237158	0.91[CHB][hapmap];0.86[YRI][hapmap]
rs2299045	0.84[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2299048	0.81[CEU][hapmap]
rs2299053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299056	0.91[CHB][hapmap]
rs3778652	0.84[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs4085876	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap]
rs4109434	0.91[CHB][hapmap]
rs7754701	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs9349978	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358059	0.93[EUR][1000 genomes]
rs9358060	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370817	0.80[CEU][hapmap]
rs9383051	0.96[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs9383054	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464785	0.90[EUR][1000 genomes]
rs9464787	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9476820	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9476827	0.84[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	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
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15365000-15402800	Weak transcription	Dnd41	blood
2	chr6:15387800-15399200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:15388000-15399200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:15390600-15399800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:15390800-15399000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:15390800-15399200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:15390800-15399200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:15390800-15399200	Weak transcription	A549	lung
9	chr6:15390800-15399400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:15390800-15400000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:15390800-15400200	Weak transcription	Aorta	Aorta
12	chr6:15391000-15399000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:15391000-15399000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:15391000-15399200	Weak transcription	HepG2	liver
15	chr6:15391000-15400000	Weak transcription	Thymus	Thymus
16	chr6:15391600-15400200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:15391800-15399200	Weak transcription	Stomach Mucosa	stomach
18	chr6:15391800-15400200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:15392000-15400200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:15392200-15399000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:15392200-15399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:15392200-15399200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:15392200-15400000	Weak transcription	NHLF	lung
24	chr6:15392400-15399000	Weak transcription	NHEK	skin
25	chr6:15392400-15399200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:15392400-15400000	Weak transcription	HMEC	breast
27	chr6:15392800-15399000	Weak transcription	Left Ventricle	heart
28	chr6:15392800-15399000	Weak transcription	Right Atrium	heart
29	chr6:15392800-15399200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:15392800-15399200	Weak transcription	Pancreas	Pancrea
31	chr6:15392800-15399200	Weak transcription	Spleen	Spleen
32	chr6:15392800-15399800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:15393000-15399000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:15393200-15399400	Weak transcription	Esophagus	oesophagus
35	chr6:15393400-15399800	Weak transcription	Fetal Brain Male	brain
36	chr6:15393400-15400000	Weak transcription	Gastric	stomach
37	chr6:15394600-15400200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:15394800-15399000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:15395000-15399200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:15395400-15399400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:15396000-15400000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr6:15396000-15400000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr6:15396200-15399200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:15396200-15400800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr6:15396200-15410200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr6:15396400-15399000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr6:15396600-15400400	Enhancers	H9 Cell Line	embryonic stem cell
48	chr6:15396800-15399200	Enhancers	Fetal Heart	heart
49	chr6:15396800-15401200	Enhancers	Small Intestine	intestine
50	chr6:15397000-15399400	Enhancers	Skeletal Muscle Female	skeletal muscle

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