Variant report

Variant	rs16876316
Chromosome Location	chr6:15407827-15407828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15402089..15404212-chr6:15407059..15409660,2	MCF-7	breast:
2	chr6:15390400..15392545-chr6:15407665..15410299,2	MCF-7	breast:
3	chr6:15401226..15405320-chr6:15407295..15410337,3	K562	blood:
4	chr6:15209991..15212845-chr6:15406600..15410606,5	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10484354	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11961516	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11961748	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11961827	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11963285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11964019	0.81[AFR][1000 genomes]
rs11964758	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11965505	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11969359	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16876327	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16876361	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35438327	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35801290	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3857641	1.00[MEX][hapmap]
rs60535196	0.95[AFR][1000 genomes]
rs6904997	1.00[MEX][hapmap]
rs6905116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6922136	1.00[MEX][hapmap]
rs73365205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73365221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73365227	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73365229	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73365234	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73367315	1.00[AMR][1000 genomes]
rs7743283	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7748631	0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs7757154	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7767966	0.86[YRI][hapmap]
rs7769123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	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
6	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
7	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
8	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
9	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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15396200-15410200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr6:15399000-15410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:15400400-15412800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:15400800-15411200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:15401200-15414000	Weak transcription	Aorta	Aorta
6	chr6:15401200-15417200	Weak transcription	Lung	lung
7	chr6:15401200-15426200	Weak transcription	Pancreas	Pancrea
8	chr6:15401400-15411600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr6:15401600-15415800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:15402600-15413600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:15403000-15409200	Weak transcription	Placenta	Placenta
12	chr6:15403000-15409400	Weak transcription	HepG2	liver
13	chr6:15403000-15413600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:15403000-15422000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:15403400-15408600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:15403600-15411400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:15404600-15409600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:15404600-15413000	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:15404600-15413400	Weak transcription	Ovary	ovary
20	chr6:15404600-15413400	Weak transcription	Osteobl	bone
21	chr6:15404600-15413600	Weak transcription	NHEK	skin
22	chr6:15404600-15413800	Weak transcription	Esophagus	oesophagus
23	chr6:15404600-15420800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:15404600-15421200	Weak transcription	Spleen	Spleen
25	chr6:15404800-15411200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:15404800-15412000	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:15404800-15413400	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:15404800-15417800	Weak transcription	NH-A	brain
29	chr6:15404800-15427600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:15404800-15429000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:15405000-15409200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:15405000-15409600	Weak transcription	Stomach Mucosa	stomach
33	chr6:15405000-15409600	Weak transcription	A549	lung
34	chr6:15405000-15413800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:15405200-15409200	Weak transcription	Fetal Intestine Large	intestine
36	chr6:15405200-15410600	Weak transcription	Primary B cells from cord blood	blood
37	chr6:15405200-15410600	Weak transcription	Small Intestine	intestine
38	chr6:15405200-15411600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:15405200-15418600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:15405400-15417000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:15405600-15409000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr6:15405600-15409000	Weak transcription	Dnd41	blood
43	chr6:15405600-15409400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:15405600-15409800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:15405600-15410600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:15405600-15411800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:15405600-15413600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:15405600-15422000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:15405800-15409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:15405800-15409200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links