Variant report

Variant	rs1556915
Chromosome Location	chr1:10242654-10242655
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	chr1:10236689..10240278-chr1:10240808..10244135,3	K562	blood:

Variant related genes	Relation type
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1002076	0.82[JPT][hapmap]
rs10492969	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs10492972	0.82[JPT][hapmap]
rs10864450	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs10864453	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs11121526	0.89[EUR][1000 genomes]
rs11121551	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12120042	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12120191	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12131441	0.82[JPT][hapmap]
rs12133617	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs12141416	0.82[JPT][hapmap]
rs12737239	0.82[JPT][hapmap]
rs12757288	0.82[JPT][hapmap]
rs1467653	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs1536262	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs1538557	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs1555849	0.82[JPT][hapmap]
rs1556916	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs1556917	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs17034643	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs17034821	0.82[JPT][hapmap]
rs17410217	0.82[JPT][hapmap]
rs1974293	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2027330	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs2039778	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2180185	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2182326	0.81[CEU][hapmap]
rs2185252	0.82[JPT][hapmap]
rs3748575	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs3748577	0.82[JPT][hapmap]
rs3748581	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs4240911	0.82[JPT][hapmap]
rs4333852	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4475756	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4529713	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4845930	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs4846196	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4846197	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4846198	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs4846199	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs4846209	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4846212	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs56221672	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6541080	0.84[CEU][hapmap]
rs6541085	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs6661326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6667639	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6696056	0.81[CEU][hapmap]
rs7418410	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs746881	0.82[JPT][hapmap]
rs7546368	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs7553935	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs8019	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs912962	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs912963	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs9332414	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs946501	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs946503	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs946504	0.88[CEU][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10230400-10245800	Weak transcription	Stomach Mucosa	stomach
2	chr1:10231200-10251600	Weak transcription	Right Atrium	heart
3	chr1:10232800-10246800	Weak transcription	Fetal Kidney	kidney
4	chr1:10233200-10258200	Weak transcription	Hela-S3	cervix
5	chr1:10234200-10249800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:10236400-10258200	Weak transcription	HSMM	muscle
7	chr1:10239000-10244600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:10239200-10242800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:10240000-10249600	Weak transcription	GM12878-XiMat	blood
10	chr1:10240000-10255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:10240200-10243600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:10240200-10246400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:10240200-10246800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:10240400-10242800	Weak transcription	K562	blood
15	chr1:10240400-10244200	Weak transcription	Primary B cells from cord blood	blood
16	chr1:10240400-10244600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:10240400-10245600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:10240400-10246400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:10240400-10246400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:10240400-10246600	Weak transcription	Fetal Brain Female	brain
21	chr1:10240400-10246800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:10240400-10250000	Weak transcription	Fetal Brain Male	brain
23	chr1:10240600-10242800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:10240600-10242800	Weak transcription	HUVEC	blood vessel
25	chr1:10240600-10243200	Weak transcription	Brain Germinal Matrix	brain
26	chr1:10240800-10243800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:10241000-10243000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:10241000-10243000	Weak transcription	NHEK	skin
29	chr1:10241000-10243200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:10241000-10244600	Weak transcription	Spleen	Spleen
31	chr1:10241000-10246800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:10241000-10248800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:10241000-10249800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:10241000-10252200	Weak transcription	HepG2	liver
35	chr1:10241000-10252400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:10241000-10254000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:10241000-10254200	Weak transcription	Brain Anterior Caudate	brain
38	chr1:10241000-10254200	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:10241000-10254200	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:10241000-10254600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:10241000-10255600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:10241000-10257200	Weak transcription	Ovary	ovary
43	chr1:10241000-10258000	Weak transcription	Psoas Muscle	Psoas
44	chr1:10241200-10242800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:10241200-10242800	Weak transcription	Fetal Thymus	thymus
46	chr1:10241200-10243000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:10241200-10243000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:10241200-10243000	Weak transcription	Adipose Nuclei	Adipose
49	chr1:10241200-10243000	Weak transcription	Aorta	Aorta
50	chr1:10241200-10243000	Weak transcription	Colonic Mucosa	Colon

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