Variant report

Variant	rs36142735
Chromosome Location	chr3:121387468-121387469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121381533..121383209-chr3:121385289..121388100,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11707716	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714406	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11716984	0.80[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719458	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11720859	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721318	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13074834	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077135	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083794	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13087578	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090660	0.89[EUR][1000 genomes]
rs1573819	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17691170	0.92[EUR][1000 genomes]
rs2070180	0.91[EUR][1000 genomes]
rs33988592	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34086988	0.91[EUR][1000 genomes]
rs34667636	0.91[EUR][1000 genomes]
rs35988617	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732408	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3772128	0.88[EUR][1000 genomes]
rs3772130	0.88[EUR][1000 genomes]
rs55643643	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55657471	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56314138	0.90[EUR][1000 genomes]
rs62268732	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62268734	0.88[ASN][1000 genomes]
rs66653099	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6791046	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7427165	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats 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	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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	39 gene(s)	inside rSNPs	diseases
7	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS 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	40 gene(s)	inside rSNPs	diseases
9	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs36142735	HCLS1	cis	Whole Blood	GTEx
rs36142735	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs36142735	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs36142735	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs36142735	IQCB1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121378000-121388400	Strong transcription	Fetal Stomach	stomach
2	chr3:121379400-121402400	Strong transcription	Fetal Intestine Large	intestine
3	chr3:121380000-121402600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:121380200-121397000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:121380400-121396400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:121380400-121396800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:121380400-121402400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:121380400-121402800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:121380400-121406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:121380600-121413800	Weak transcription	Stomach Mucosa	stomach
11	chr3:121380800-121389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:121381000-121388200	Strong transcription	Fetal Intestine Small	intestine
13	chr3:121381000-121391400	Strong transcription	GM12878-XiMat	blood
14	chr3:121381000-121401800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:121381000-121403200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:121381400-121388400	Strong transcription	Gastric	stomach
17	chr3:121381400-121389000	Strong transcription	Thymus	Thymus
18	chr3:121381400-121389800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:121381400-121406800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:121381600-121388200	Strong transcription	Lung	lung
21	chr3:121381600-121388400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:121381600-121388600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:121381600-121388800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr3:121381600-121389000	Strong transcription	Fetal Brain Female	brain
25	chr3:121381600-121389200	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr3:121381600-121389200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:121381600-121389400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:121381600-121389600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:121381600-121391800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:121381600-121396600	Strong transcription	Fetal Thymus	thymus
31	chr3:121381600-121396800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:121381600-121396800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr3:121381600-121401600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr3:121381600-121402200	Strong transcription	Placenta	Placenta
35	chr3:121381600-121402400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr3:121381600-121402400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:121381600-121402600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr3:121381600-121402800	Strong transcription	Liver	Liver
39	chr3:121381800-121388000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:121381800-121388200	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr3:121381800-121388400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:121381800-121388400	Strong transcription	Spleen	Spleen
43	chr3:121381800-121390200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:121381800-121390600	Strong transcription	Osteobl	bone
45	chr3:121381800-121396600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:121381800-121401200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:121381800-121402600	Strong transcription	Primary T cells from cord blood	blood
48	chr3:121382000-121388400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:121382000-121389200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:121382000-121401800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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