Variant report

Variant	rs35225534
Chromosome Location	chr3:142118642-142118643
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	chr3:142085151..142088133-chr3:142116626..142119405,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs62276397	0.90[AMR][1000 genomes]
rs7349528	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv522549	chr3:141812759-142164735	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv877557	chr3:142090402-142150204	Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
9	esv2036616	chr3:142118643-142118644	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35225534	SIGLECP16	trans	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142076000-142136400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:142076800-142120200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:142076800-142138200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:142083600-142158600	Weak transcription	NHEK	skin
5	chr3:142105000-142151800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:142105600-142123000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:142105800-142136600	Strong transcription	Fetal Intestine Large	intestine
8	chr3:142106800-142123000	Weak transcription	Fetal Brain Male	brain
9	chr3:142106800-142150800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:142109200-142141800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:142112200-142119400	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr3:142112200-142133200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr3:142112200-142145000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:142112200-142145400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:142112200-142151600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:142112200-142152000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:142112200-142152200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:142112200-142154600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:142112400-142119200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:142112400-142119200	Strong transcription	Primary B cells from cord blood	blood
21	chr3:142112400-142120200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr3:142112400-142120800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:142112400-142142400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr3:142112400-142146600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:142112600-142141600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:142112600-142150600	Strong transcription	Placenta	Placenta
27	chr3:142112800-142121200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:142112800-142142800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:142113000-142119600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:142113000-142152200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:142113200-142119000	Strong transcription	GM12878-XiMat	blood
32	chr3:142113400-142151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:142113400-142151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:142113800-142119600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:142114600-142120000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:142114600-142126600	Weak transcription	Fetal Heart	heart
37	chr3:142114800-142151800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:142115200-142126600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:142115200-142129400	Weak transcription	Small Intestine	intestine
40	chr3:142115600-142119000	Weak transcription	HUVEC	blood vessel
41	chr3:142115800-142119200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:142115800-142120400	Weak transcription	Ovary	ovary
43	chr3:142115800-142123200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:142115800-142123400	Weak transcription	K562	blood
45	chr3:142115800-142125200	Weak transcription	Psoas Muscle	Psoas
46	chr3:142115800-142125400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:142115800-142125400	Weak transcription	Aorta	Aorta
48	chr3:142115800-142125400	Weak transcription	Lung	lung
49	chr3:142115800-142125400	Weak transcription	Spleen	Spleen
50	chr3:142115800-142126600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links