Variant report

Variant	rs1556971
Chromosome Location	chr10:99527846-99527847
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99523562..99525192-chr10:99527348..99530320,2	MCF-7	breast:
2	chr10:99526747..99528824-chr10:99529529..99531423,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10748709	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786367	0.85[CEU][hapmap]
rs10786370	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10786371	0.82[JPT][hapmap]
rs10786372	0.81[CEU][hapmap]
rs10786373	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10786374	0.81[EUR][1000 genomes]
rs10882993	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10882995	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs10882996	0.84[EUR][1000 genomes]
rs10882997	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882998	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11189353	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs11189355	0.95[CEU][hapmap]
rs11189357	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs11189359	0.94[CEU][hapmap];0.83[JPT][hapmap]
rs11189360	1.00[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs11189361	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11189362	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189367	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11189374	0.81[EUR][1000 genomes]
rs11189377	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11815012	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12412543	0.84[EUR][1000 genomes]
rs12569711	0.85[EUR][1000 genomes]
rs12569757	0.82[ASN][1000 genomes]
rs12783992	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981237	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1981238	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2010732	0.88[ASN][1000 genomes]
rs2027376	0.88[ASN][1000 genomes]
rs2039826	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34283185	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750612	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3750614	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs3750615	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs3814558	0.82[CEU][hapmap]
rs3814559	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3814560	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4244329	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4244330	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4917786	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4919139	0.96[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072751	0.97[ASN][1000 genomes]
rs7080894	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7080953	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7081652	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094519	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7099540	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7100453	0.82[EUR][1000 genomes]
rs7478323	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7907679	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7910589	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7916164	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7916454	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs7916593	0.88[ASN][1000 genomes]
rs7922907	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs883324	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs946777	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs946778	0.80[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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99520200-99528400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:99520400-99529200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:99520400-99530400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr10:99520600-99528400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr10:99521600-99528200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr10:99522200-99528000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr10:99522200-99530800	Weak transcription	Right Ventricle	heart
8	chr10:99522400-99528200	Weak transcription	Aorta	Aorta
9	chr10:99522400-99528400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:99522400-99529000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr10:99522400-99530200	Weak transcription	A549	lung
12	chr10:99522600-99528400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr10:99522600-99530000	Weak transcription	Fetal Intestine Large	intestine
14	chr10:99522600-99530400	Weak transcription	Primary T cells from cord blood	blood
15	chr10:99522800-99528200	Weak transcription	Colonic Mucosa	Colon
16	chr10:99522800-99529400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr10:99523200-99528200	Weak transcription	Brain Germinal Matrix	brain
18	chr10:99523200-99530400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:99523400-99528000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:99523400-99529000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr10:99523600-99528000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr10:99523600-99528800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr10:99524200-99530200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:99524600-99528200	Weak transcription	Primary B cells from cord blood	blood
25	chr10:99524600-99528800	Weak transcription	Thymus	Thymus
26	chr10:99524800-99529200	Weak transcription	GM12878-XiMat	blood
27	chr10:99525000-99530400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr10:99525400-99529000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr10:99525400-99529000	Strong transcription	Fetal Intestine Small	intestine
30	chr10:99525600-99528400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:99525600-99528600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr10:99525800-99530400	Weak transcription	HSMM	muscle
33	chr10:99526200-99528600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:99526400-99528000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr10:99526400-99531200	Weak transcription	K562	blood
36	chr10:99527000-99528800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:99527200-99528000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:99527200-99528800	Genic enhancers	Pancreas	Pancrea
39	chr10:99527600-99530600	Weak transcription	Gastric	stomach
40	chr10:99527800-99528000	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links