Variant report

Variant	rs1852859
Chromosome Location	chr7:26381207-26381208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26239072..26241329-chr7:26379066..26381218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122565	Chromatin interaction
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10230728	0.80[ASN][1000 genomes]
rs10231242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10238717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10246401	0.80[ASN][1000 genomes]
rs10252532	0.84[ASN][1000 genomes]
rs10260489	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10270099	0.84[ASN][1000 genomes]
rs10270279	0.84[ASN][1000 genomes]
rs10281957	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10951130	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12532077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12534816	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534835	0.84[EUR][1000 genomes]
rs12537520	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12666571	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12669655	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12670125	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12673873	0.84[EUR][1000 genomes]
rs13243295	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13243466	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13244200	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1852860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014728	0.84[EUR][1000 genomes]
rs2014729	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2391276	0.82[ASN][1000 genomes]
rs35042524	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3801890	0.81[ASN][1000 genomes]
rs3801891	0.81[ASN][1000 genomes]
rs4506105	0.82[ASN][1000 genomes]
rs6947348	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7784736	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv1021308	chr7:26116605-26419720	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv2761313	chr7:26340970-26389772	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26335200-26386400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:26345600-26386200	Weak transcription	Thymus	Thymus
3	chr7:26361800-26385400	Weak transcription	Pancreas	Pancrea
4	chr7:26368800-26405000	Weak transcription	Placenta	Placenta
5	chr7:26370400-26385000	Weak transcription	Spleen	Spleen
6	chr7:26372400-26405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:26374400-26386200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:26374800-26382600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:26374800-26386200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr7:26375000-26414000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:26375200-26385000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:26375200-26386200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:26376400-26385800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:26376600-26385200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr7:26377400-26382600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr7:26377400-26385600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:26377600-26386000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:26377800-26386200	Weak transcription	GM12878-XiMat	blood
19	chr7:26378400-26384600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:26378800-26382600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr7:26379000-26386200	Weak transcription	Fetal Intestine Small	intestine
22	chr7:26380000-26382800	Weak transcription	Primary B cells from cord blood	blood
23	chr7:26380400-26382400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr7:26380400-26386000	Weak transcription	Primary T cells from cord blood	blood
25	chr7:26380600-26385000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:26380800-26381600	Enhancers	Primary B cells from peripheral blood	blood
27	chr7:26380800-26382600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr7:26381000-26386200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:26381200-26382400	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links