Variant report

Variant	rs16876354
Chromosome Location	chr6:15440983-15440984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15249702..15251609-chr6:15440031..15441697,2	MCF-7	breast:
2	chr6:15246180..15248927-chr6:15440095..15442799,2	K562	blood:
3	chr6:15433530..15436747-chr6:15439990..15443191,3	K562	blood:
4	chr6:15425552..15427060-chr6:15439527..15441098,2	K562	blood:
5	chr6:15432414..15437643-chr6:15439715..15443191,6	K562	blood:
6	chr6:15436867..15438736-chr6:15439422..15441651,2	MCF-7	breast:
7	chr6:15409321..15411369-chr6:15440197..15441941,2	K562	blood:

Variant related genes	Relation type
ENSG00000235488	Chromatin interaction
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10484355	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10949294	1.00[JPT][hapmap]
rs10949295	1.00[JPT][hapmap]
rs11756544	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11757415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11759478	0.88[JPT][hapmap]
rs12211278	1.00[JPT][hapmap]
rs13192347	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13194410	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs13195950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13205396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13205612	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13208486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13214720	0.89[EUR][1000 genomes]
rs16876278	1.00[JPT][hapmap]
rs17468929	0.86[CEU][hapmap]
rs17575737	0.86[JPT][hapmap]
rs17576233	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17576436	0.88[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17576710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17637773	1.00[JPT][hapmap]
rs17638192	0.88[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17638720	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299057	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34002211	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34764533	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35047303	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35139070	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35364784	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35629999	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35734069	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35918625	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56123857	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60416461	0.81[AFR][1000 genomes]
rs61296041	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66478504	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6904997	0.95[YRI][hapmap]
rs6914974	0.95[YRI][hapmap]
rs6922136	0.95[YRI][hapmap]
rs6941859	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72836327	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742102	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7747437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767966	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15417000-15452200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr6:15424600-15442000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr6:15425600-15445400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:15426000-15441000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:15426400-15442000	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:15427000-15450800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr6:15428000-15441800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:15428800-15441600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr6:15429200-15446000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:15430800-15441000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr6:15430800-15441600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:15431000-15441600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:15431800-15441600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:15432400-15441600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:15433000-15443200	Weak transcription	Hela-S3	cervix
16	chr6:15434000-15441800	Enhancers	Primary T cells from cord blood	blood
17	chr6:15434000-15441800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:15434400-15441600	Weak transcription	Ovary	ovary
19	chr6:15434400-15444400	Weak transcription	HSMMtube	muscle
20	chr6:15435000-15448000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:15435800-15443400	Weak transcription	HepG2	liver
22	chr6:15435800-15445400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:15435800-15446000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:15435800-15453600	Weak transcription	Fetal Intestine Small	intestine
25	chr6:15435800-15487600	Weak transcription	Colonic Mucosa	Colon
26	chr6:15436000-15441600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:15436000-15447000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:15436200-15442000	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:15436600-15441400	Weak transcription	Liver	Liver
30	chr6:15437000-15441800	Enhancers	Fetal Heart	heart
31	chr6:15437000-15444000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:15437400-15444400	Weak transcription	Lung	lung
33	chr6:15437600-15441600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:15437600-15444200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:15437800-15444400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:15438000-15441400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:15438000-15441600	Enhancers	Dnd41	blood
38	chr6:15438200-15441000	Enhancers	Primary T cells fromperipheralblood	blood
39	chr6:15438200-15441000	Enhancers	Brain Cingulate Gyrus	brain
40	chr6:15438200-15444400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:15438400-15441800	Enhancers	Brain Substantia Nigra	brain
42	chr6:15438600-15441600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:15438600-15441800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:15438600-15441800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:15438600-15442000	Enhancers	Fetal Thymus	thymus
46	chr6:15438600-15442400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:15438600-15442600	Weak transcription	Fetal Brain Male	brain
48	chr6:15438600-15444400	Weak transcription	Spleen	Spleen
49	chr6:15438800-15441000	Enhancers	Fetal Muscle Leg	muscle
50	chr6:15438800-15443600	Enhancers	K562	blood

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