Variant report

Variant	rs11721318
Chromosome Location	chr3:121429485-121429486
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	chr3:121429333..121431027-chr3:121468006..121470024,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11706783	0.96[CEU][hapmap]
rs11707504	0.82[EUR][1000 genomes]
rs11707518	0.82[EUR][1000 genomes]
rs11707716	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714406	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11715951	0.81[EUR][1000 genomes]
rs11716984	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719093	0.82[EUR][1000 genomes]
rs11719458	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11720859	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13061326	0.82[EUR][1000 genomes]
rs13062684	0.82[EUR][1000 genomes]
rs13072618	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072767	0.82[EUR][1000 genomes]
rs13074834	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077135	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083794	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13087578	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090660	0.87[EUR][1000 genomes]
rs13090798	0.82[EUR][1000 genomes]
rs13433692	0.82[EUR][1000 genomes]
rs13434284	0.82[EUR][1000 genomes]
rs1573819	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17691170	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs1920320	0.91[CEU][hapmap]
rs2070180	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs28660600	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs28674947	0.81[EUR][1000 genomes]
rs33988592	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34086988	0.88[EUR][1000 genomes]
rs34667636	0.88[EUR][1000 genomes]
rs35679661	0.82[EUR][1000 genomes]
rs35988617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36142735	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732408	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772128	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs3772130	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs3805127	0.91[CEU][hapmap]
rs4280673	0.81[EUR][1000 genomes]
rs4298081	0.81[EUR][1000 genomes]
rs4311252	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4413346	0.82[EUR][1000 genomes]
rs55643643	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55657471	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56314138	0.88[EUR][1000 genomes]
rs62268732	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62268734	0.92[ASN][1000 genomes]
rs66653099	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768621	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6776670	0.96[CEU][hapmap]
rs6791046	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427165	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289177	0.80[EUR][1000 genomes]
rs9812228	0.82[EUR][1000 genomes]
rs9816844	0.81[EUR][1000 genomes]
rs9826473	0.96[CEU][hapmap]
rs9839617	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9841595	0.82[EUR][1000 genomes]
rs9856641	0.91[CEU][hapmap]
rs9878086	0.82[EUR][1000 genomes]
rs9883467	0.96[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	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
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11721318	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs11721318	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs11721318	HCLS1	cis	Whole Blood	GTEx
rs11721318	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs11721318	IQCB1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
3	chr3:121399000-121440400	Weak transcription	K562	blood
4	chr3:121401200-121434000	Weak transcription	Gastric	stomach
5	chr3:121404000-121432800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:121410400-121435600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:121411000-121432000	Weak transcription	NHEK	skin
8	chr3:121411000-121432800	Weak transcription	Fetal Brain Male	brain
9	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:121411400-121432800	Weak transcription	Colonic Mucosa	Colon
11	chr3:121411400-121437200	Weak transcription	Small Intestine	intestine
12	chr3:121413400-121446200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:121414800-121436200	Weak transcription	Stomach Mucosa	stomach
14	chr3:121417200-121430800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:121417200-121435800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:121417400-121431600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:121417600-121430800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:121417600-121431600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:121417600-121432000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:121417600-121432000	Weak transcription	Fetal Brain Female	brain
21	chr3:121417600-121432800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:121417600-121432800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:121417600-121434200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:121417600-121434200	Weak transcription	Aorta	Aorta
25	chr3:121417600-121435200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:121417600-121437200	Weak transcription	Spleen	Spleen
27	chr3:121417800-121431600	Weak transcription	HSMMtube	muscle
28	chr3:121418000-121432000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:121418000-121434200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:121418000-121435400	Weak transcription	NHLF	lung
31	chr3:121418800-121442000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:121419600-121436200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:121419800-121434400	Weak transcription	HUVEC	blood vessel
34	chr3:121420200-121432600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:121420200-121433000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:121420400-121432000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:121420800-121430800	Weak transcription	Fetal Kidney	kidney
38	chr3:121420800-121432000	Weak transcription	Brain Germinal Matrix	brain
39	chr3:121421000-121430800	Weak transcription	NH-A	brain
40	chr3:121421000-121431200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:121421000-121432000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:121421000-121432000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:121421000-121432600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:121421200-121431000	Weak transcription	GM12878-XiMat	blood
45	chr3:121421200-121431000	Weak transcription	HepG2	liver
46	chr3:121421200-121431800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:121421200-121435200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:121421400-121431400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:121421400-121431400	Weak transcription	Brain Substantia Nigra	brain
50	chr3:121421400-121431600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links