Variant report

Variant	rs1004228
Chromosome Location	chr8:54795241-54795242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:54792772..54795313-chr8:55047110..55049629,2	MCF-7	breast:
2	chr8:54794718..54796302-chr8:54804147..54805948,2	K562	blood:

Variant related genes	Relation type
ENSG00000137547	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10504158	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11985729	0.81[ASN][1000 genomes]
rs1384797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483538	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1483539	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1483540	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1483542	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16919616	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1842982	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1842983	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1842984	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2062226	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306584	0.94[EUR][1000 genomes]
rs3824121	1.00[CEU][hapmap]
rs4518622	0.92[ASN][1000 genomes]
rs57546155	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57553178	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58652215	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60696924	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60819522	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61194604	0.82[ASN][1000 genomes]
rs61231337	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61433056	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6473894	1.00[CEU][hapmap]
rs6994332	0.82[ASN][1000 genomes]
rs6997050	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6998532	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7016171	0.82[ASN][1000 genomes]
rs7017291	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7017967	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73680325	0.94[EUR][1000 genomes]
rs73680341	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73680342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73680346	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7827611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7831399	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7846259	1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021775	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv539621	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54791200-54795600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:54791800-54795400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr8:54791800-54795600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr8:54792000-54795400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
5	chr8:54792000-54795400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
6	chr8:54792200-54795400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
7	chr8:54792200-54795400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
8	chr8:54792200-54795600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr8:54792800-54795400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr8:54792800-54795400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
11	chr8:54792800-54796400	Active TSS	GM12878-XiMat	blood
12	chr8:54793000-54795400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr8:54793600-54795600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
14	chr8:54793800-54795400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:54793800-54795400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:54793800-54795400	Bivalent Enhancer	Spleen	Spleen
17	chr8:54793800-54795600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr8:54794000-54795400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
19	chr8:54794000-54795600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr8:54794200-54795400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
21	chr8:54794200-54795600	Active TSS	Brain Anterior Caudate	brain
22	chr8:54794400-54795400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
23	chr8:54794400-54795400	Bivalent Enhancer	Liver	Liver
24	chr8:54794400-54795400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr8:54794400-54795400	Bivalent Enhancer	Lung	lung
26	chr8:54794400-54795400	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr8:54794400-54795600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr8:54794400-54795600	Bivalent Enhancer	Fetal Lung	lung
29	chr8:54794600-54795400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr8:54794600-54795400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr8:54794600-54795400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr8:54794600-54795600	Flanking Active TSS	HUVEC	blood vessel
33	chr8:54794800-54795400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr8:54794800-54795400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr8:54794800-54795400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:54794800-54795400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr8:54794800-54795400	Enhancers	Gastric	stomach
38	chr8:54794800-54795600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
39	chr8:54794800-54795600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
40	chr8:54794800-54795600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
41	chr8:54794800-54795600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr8:54794800-54795600	Flanking Active TSS	HMEC	breast
43	chr8:54794800-54795600	Flanking Active TSS	NH-A	brain
44	chr8:54795000-54795400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
45	chr8:54795000-54795400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
46	chr8:54795000-54795400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr8:54795000-54795400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
48	chr8:54795000-54795400	Bivalent Enhancer	Fetal Intestine Large	intestine
49	chr8:54795000-54795600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
50	chr8:54795000-54795600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links