Variant report

Variant	rs7554557
Chromosome Location	chr1:56969857-56969858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:56967555..56969959-chr1:56994759..56997021,2	K562	blood:
2	chr1:56968459..56970187-chr1:56994690..56997021,2	K562	blood:
3	chr1:56968634..56970634-chr1:57041979..57044955,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10157636	0.82[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10888977	0.81[JPT][hapmap]
rs11583161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11590570	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12081589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12084507	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4912305	0.85[EUR][1000 genomes]
rs4912307	0.85[EUR][1000 genomes]
rs4912314	0.95[JPT][hapmap]
rs57966457	0.85[ASN][1000 genomes]
rs58289463	0.90[ASN][1000 genomes]
rs60314060	0.85[ASN][1000 genomes]
rs6690245	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs72664306	0.85[EUR][1000 genomes]
rs72664313	0.85[EUR][1000 genomes]
rs72664316	0.85[EUR][1000 genomes]
rs72664330	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7512545	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7515808	0.95[JPT][hapmap]
rs7519268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7549894	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56957400-56971800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:56957600-56971800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:56957800-56971800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:56957800-56975600	Weak transcription	Fetal Brain Female	brain
5	chr1:56958000-56975600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:56958000-56977000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:56958200-56971600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:56958800-56971600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:56959400-56972000	Strong transcription	Fetal Stomach	stomach
10	chr1:56959800-56972800	Weak transcription	Dnd41	blood
11	chr1:56960800-56976000	Genic enhancers	HepG2	liver
12	chr1:56961400-56971400	Weak transcription	Primary B cells from cord blood	blood
13	chr1:56961400-56972600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:56961400-56972800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:56961600-56971800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:56961800-56971600	Weak transcription	Colonic Mucosa	Colon
17	chr1:56962000-56971400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:56962000-56971800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:56962400-56970200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:56962400-56970800	Weak transcription	HSMMtube	muscle
21	chr1:56962400-56971600	Weak transcription	Esophagus	oesophagus
22	chr1:56962400-56971600	Weak transcription	Ovary	ovary
23	chr1:56962400-56971600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:56962400-56976000	Weak transcription	NH-A	brain
25	chr1:56962600-56972200	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:56962800-56970800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:56962800-56970800	Weak transcription	Fetal Kidney	kidney
28	chr1:56963000-56971600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:56963600-56970600	Weak transcription	Gastric	stomach
30	chr1:56963600-56971000	Weak transcription	Thymus	Thymus
31	chr1:56964000-56971400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:56964200-56971600	Weak transcription	Stomach Mucosa	stomach
33	chr1:56964200-56972600	Weak transcription	Small Intestine	intestine
34	chr1:56964800-56976000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:56964800-56979200	Genic enhancers	NHDF-Ad	bronchial
36	chr1:56965000-56975600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:56965200-56971800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:56965200-56972200	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr1:56965200-56975600	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr1:56965200-56975600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:56965800-56975600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:56965800-56975800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:56966000-56970200	Genic enhancers	Right Ventricle	heart
44	chr1:56966000-56980600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:56966400-56971600	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:56966800-56974600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:56966800-56975800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:56967200-56970400	Strong transcription	Fetal Intestine Large	intestine
50	chr1:56967200-56971800	Strong transcription	HSMM	muscle

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