Variant report

Variant	rs16891477
Chromosome Location	chr6:26240752-26240753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29191314..29194018-chr6:26240540..26242629,2	MCF-7	breast:
2	chr22:31890586..31892478-chr6:26238591..26241305,2	MCF-7	breast:
3	chr17:57908611..57910450-chr6:26240624..26243360,2	MCF-7	breast:
4	chr6:26239694..26242322-chr6:27777382..27779315,2	MCF-7	breast:
5	chr6:26238918..26240875-chr6:27113919..27116151,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000265565	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1000308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484437	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1341758	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16891404	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16891417	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs16891421	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16891427	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16891440	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16891450	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16891453	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16891458	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16891471	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16891497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17533076	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17600910	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34550794	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3818947	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs41266803	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41266805	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4593350	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs55856153	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56360223	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56372675	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61910695	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6913828	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs989710	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
8	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
9	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
10	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
11	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
12	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
13	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
14	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
15	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
16	nsv1021294	chr6:26190316-26246784	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	309 gene(s)	inside rSNPs	diseases
17	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26237400-26244000	Weak transcription	Dnd41	blood
2	chr6:26240000-26240800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:26240000-26241200	Active TSS	Fetal Intestine Large	intestine
4	chr6:26240000-26241200	Active TSS	Fetal Intestine Small	intestine
5	chr6:26240000-26241200	Active TSS	Fetal Stomach	stomach
6	chr6:26240000-26241400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:26240000-26241800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:26240000-26241800	Active TSS	Fetal Brain Female	brain
9	chr6:26240000-26241800	Active TSS	NH-A	brain
10	chr6:26240000-26242000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:26240000-26242200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:26240200-26240800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr6:26240200-26240800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:26240200-26240800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
15	chr6:26240200-26241000	Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:26240200-26241000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:26240200-26241000	Active TSS	Placenta	Placenta
18	chr6:26240200-26241000	Flanking Active TSS	HMEC	breast
19	chr6:26240200-26241000	Flanking Active TSS	HUVEC	blood vessel
20	chr6:26240200-26241200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:26240200-26241200	Active TSS	Fetal Lung	lung
22	chr6:26240200-26241200	Active TSS	Fetal Muscle Trunk	muscle
23	chr6:26240200-26241400	Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr6:26240200-26241400	Bivalent/Poised TSS	Liver	Liver
25	chr6:26240200-26241400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
26	chr6:26240200-26241400	ZNF genes & repeats	Fetal Brain Male	brain
27	chr6:26240200-26241400	Active TSS	Thymus	Thymus
28	chr6:26240200-26241400	Flanking Active TSS	GM12878-XiMat	blood
29	chr6:26240200-26241400	Active TSS	HSMMtube	muscle
30	chr6:26240200-26241600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr6:26240200-26241600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr6:26240200-26241600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:26240200-26241600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
34	chr6:26240200-26241600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
35	chr6:26240200-26241600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
36	chr6:26240200-26241600	Active TSS	Placenta Amnion	Placenta Amnion
37	chr6:26240200-26241600	Bivalent/Poised TSS	NHDF-Ad	bronchial
38	chr6:26240200-26241600	Active TSS	NHLF	lung
39	chr6:26240200-26241800	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:26240200-26241800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:26240200-26241800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:26240200-26241800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:26240200-26241800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:26240200-26241800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr6:26240200-26241800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr6:26240200-26241800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr6:26240200-26241800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:26240200-26241800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:26240200-26241800	Active TSS	Aorta	Aorta
50	chr6:26240200-26241800	Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links