Variant report

Variant	rs3857641
Chromosome Location	chr6:15343109-15343110
allele	A/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	chr6:15340578..15343922-chr6:15348379..15351568,3	K562	blood:
2	chr6:15342583..15344777-chr6:15361568..15363070,2	K562	blood:
3	chr6:15341234..15343785-chr6:15346547..15348228,2	MCF-7	breast:
4	chr6:15340747..15343186-chr6:15343295..15345820,2	K562	blood:
5	chr6:15342546..15345320-chr6:15399209..15400740,2	K562	blood:
6	chr6:15339473..15343526-chr6:15347239..15351934,4	K562	blood:
7	chr6:15336788..15338488-chr6:15341529..15343382,2	K562	blood:
8	chr6:15298447..15300545-chr6:15342591..15344623,2	K562	blood:
9	chr6:15245967..15248846-chr6:15342706..15344911,2	K562	blood:
10	chr6:15326922..15329767-chr6:15340745..15343836,3	K562	blood:
11	chr6:15342018..15344777-chr6:15361568..15363151,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10484354	1.00[MEX][hapmap]
rs11968075	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11969359	1.00[MEX][hapmap]
rs16876233	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16876316	1.00[MEX][hapmap]
rs16876327	1.00[MEX][hapmap]
rs56156626	1.00[AMR][1000 genomes]
rs58053975	1.00[AMR][1000 genomes]
rs6904997	1.00[MEX][hapmap]
rs6922136	1.00[MEX][hapmap]
rs707829	0.90[YRI][hapmap]
rs707836	0.89[ASW][hapmap];0.87[LWK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs73361549	1.00[AMR][1000 genomes]
rs73361569	1.00[AMR][1000 genomes]
rs73361576	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7757154	1.00[MEX][hapmap]
rs794777	0.82[YRI][hapmap]
rs794778	0.82[YRI][hapmap]
rs794783	0.82[YRI][hapmap]
rs794785	0.89[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15327800-15375800	Weak transcription	Aorta	Aorta
2	chr6:15329800-15343600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:15330800-15348800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:15331600-15345400	Weak transcription	Ovary	ovary
5	chr6:15331600-15346000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:15331600-15347000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:15332000-15355800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:15332000-15359400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:15333200-15351400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:15333800-15347600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:15334800-15350200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:15335400-15349800	Enhancers	Fetal Thymus	thymus
13	chr6:15337800-15346400	Weak transcription	NHDF-Ad	bronchial
14	chr6:15338000-15351600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:15338400-15349800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:15338400-15351600	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:15338600-15343800	Weak transcription	Right Ventricle	heart
18	chr6:15338800-15350600	Weak transcription	Adipose Nuclei	Adipose
19	chr6:15338800-15351600	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:15339400-15343600	Weak transcription	Fetal Lung	lung
21	chr6:15339400-15351600	Weak transcription	Right Atrium	heart
22	chr6:15339600-15347000	Weak transcription	Spleen	Spleen
23	chr6:15340000-15344200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:15340000-15344600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr6:15340000-15344800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr6:15340000-15344800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:15340000-15346200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:15340000-15347000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr6:15340000-15347200	Enhancers	Primary B cells from peripheral blood	blood
30	chr6:15340200-15344200	Enhancers	Psoas Muscle	Psoas
31	chr6:15340600-15343400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:15340800-15344400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr6:15341000-15362800	Weak transcription	Fetal Intestine Small	intestine
34	chr6:15341200-15343400	Enhancers	K562	blood
35	chr6:15341200-15343800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:15341200-15346800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:15341200-15349200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:15341200-15359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:15341400-15348000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:15341400-15365400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:15341600-15343600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:15341600-15343800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:15341600-15349000	Weak transcription	NHLF	lung
44	chr6:15341600-15349400	Enhancers	Primary hematopoietic stem cells	blood
45	chr6:15341600-15350800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr6:15341600-15352200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:15341800-15343600	Weak transcription	Thymus	Thymus
48	chr6:15341800-15343800	Weak transcription	Fetal Stomach	stomach
49	chr6:15341800-15344200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr6:15341800-15344400	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links