Variant report

Variant	rs1886239
Chromosome Location	chr6:161859883-161859884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161848154..161849846-chr6:161859403..161861110,2	MCF-7	breast:
2	chr6:161859122..161861758-chr6:161866811..161869668,2	MCF-7	breast:
3	chr6:161855024..161858360-chr6:161858723..161860898,4	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1886238	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs58063982	1.00[AMR][1000 genomes]
rs73600931	1.00[AMR][1000 genomes]
rs73600947	1.00[AMR][1000 genomes]
rs73600950	1.00[AMR][1000 genomes]
rs7758262	1.00[AMR][1000 genomes]
rs7758417	1.00[AMR][1000 genomes]
rs9456667	1.00[AMR][1000 genomes]
rs9456668	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9456669	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9456670	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9458259	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv481931	chr6:161647026-161961906	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1031234	chr6:161676768-162250726	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv886819	chr6:161712035-162520133	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv886820	chr6:161712880-162184932	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv830854	chr6:161739926-161927515	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv518931	chr6:161793319-162406335	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv481861	chr6:161802883-162160197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1033192	chr6:161812419-161860010	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1024921	chr6:161814295-161860636	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2761040	chr6:161814307-161860636	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv520078	chr6:161814907-161860010	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv605066	chr6:161814907-161860010	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv481930	chr6:161815297-161860058	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv605067	chr6:161816660-161860010	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1022345	chr6:161816661-161860010	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1018065	chr6:161816661-161860169	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1018466	chr6:161816661-161860636	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv605068	chr6:161817168-161860010	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1023319	chr6:161817703-161860636	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv481981	chr6:161829077-162215745	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1015211	chr6:161836242-161860636	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv1033603	chr6:161844266-162001436	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv481750	chr6:161850976-161996586	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1886239	DAB2	trans	lymphoblastoid	seeQTL
rs1886239	ARHGAP20	trans	lymphoblastoid	seeQTL
rs1886239	HNMT	trans	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161855600-161864400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:161855800-161860200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:161856000-161860000	Enhancers	NH-A	brain
4	chr6:161856000-161861600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:161856200-161860200	Weak transcription	Left Ventricle	heart
6	chr6:161856400-161860000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:161856400-161860000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:161856400-161860200	Weak transcription	Ovary	ovary
9	chr6:161856600-161860000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:161856600-161866200	Weak transcription	Psoas Muscle	Psoas
11	chr6:161856800-161860000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:161856800-161860000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:161856800-161860000	Weak transcription	Osteobl	bone
14	chr6:161856800-161860200	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:161856800-161861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:161857000-161860000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:161857400-161860000	Enhancers	HMEC	breast
18	chr6:161857800-161863400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:161858000-161860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:161858400-161860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:161858400-161862800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:161859000-161860000	Enhancers	HSMM	muscle
23	chr6:161859000-161860200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:161859400-161860200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:161859400-161860600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:161859600-161860000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:161859600-161860000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:161859600-161860000	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:161859600-161860000	Enhancers	Fetal Brain Female	brain
30	chr6:161859600-161860000	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:161859600-161860000	Weak transcription	Pancreas	Pancrea
32	chr6:161859800-161860000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr6:161859800-161860000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:161859800-161860000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr6:161859800-161860000	Enhancers	Brain Angular Gyrus	brain
36	chr6:161859800-161860000	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr6:161859800-161860000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr6:161859800-161860000	Enhancers	Fetal Brain Male	brain
39	chr6:161859800-161860000	Enhancers	Fetal Kidney	kidney
40	chr6:161859800-161860000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr6:161859800-161860000	Flanking Active TSS	A549	lung
42	chr6:161859800-161860000	Bivalent Enhancer	K562	blood
43	chr6:161859800-161860200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:161859800-161860200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr6:161859800-161860200	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr6:161859800-161860200	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr6:161859800-161860600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:161859800-161860600	Active TSS	Brain Substantia Nigra	brain
49	chr6:161859800-161860600	Flanking Active TSS	HSMMtube	muscle
50	chr6:161859800-161860600	Flanking Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links