Variant report

Variant	rs2759662
Chromosome Location	chr1:197361571-197361572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197360270..197362216-chr1:197363552..197365582,2	K562	blood:
2	chr1:197360686..197361661-chr1:197369304..197369843,2	MCF-7	breast:
3	chr1:197360719..197363248-chr1:197366625..197368316,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10754222	0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10801604	0.95[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10801605	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs10922213	0.88[CEU][hapmap]
rs10922215	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10922216	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10922221	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10922223	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10922225	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583319	0.88[JPT][hapmap]
rs11799515	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs11802794	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs12083773	0.95[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12128912	0.94[CEU][hapmap]
rs17621130	0.87[JPT][hapmap]
rs2476020	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2494268	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2494271	0.95[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap]
rs2759655	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2759663	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2759665	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2821102	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2821108	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2821121	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs34241991	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35367258	0.91[EUR][1000 genomes]
rs66619347	0.89[EUR][1000 genomes]
rs7522325	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197354400-197366000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:197358600-197362200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr1:197358600-197362400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr1:197358600-197362600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:197358800-197361800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:197358800-197362000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr1:197358800-197362200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:197358800-197362600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:197358800-197362800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:197359400-197362000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:197359800-197361600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:197360600-197363400	Enhancers	Primary T cells from cord blood	blood
13	chr1:197361000-197362000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:197361000-197362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:197361200-197361600	Enhancers	Dnd41	blood
16	chr1:197361400-197362200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:197361400-197362200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:197361400-197362400	Weak transcription	Fetal Thymus	thymus
19	chr1:197361400-197368800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links