Variant report

Variant	rs6768621
Chromosome Location	chr3:121530274-121530275
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121507997..121509959-chr3:121529040..121530668,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10934559	0.86[YRI][hapmap]
rs11706783	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707504	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707518	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714406	0.95[CEU][hapmap]
rs11715951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717483	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719093	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719458	0.96[CEU][hapmap]
rs11721291	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11721318	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs13061326	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062684	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065245	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13072767	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074834	0.81[EUR][1000 genomes]
rs13083794	0.96[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13087578	0.96[CEU][hapmap]
rs13090798	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098883	0.92[ASN][1000 genomes]
rs1318472	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13433692	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434284	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573819	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17691170	0.96[CEU][hapmap]
rs17742508	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1920320	0.96[CEU][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070180	0.95[CEU][hapmap]
rs28660600	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28674947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33988592	0.81[EUR][1000 genomes]
rs34865234	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35359572	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs35679661	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35988617	0.81[EUR][1000 genomes]
rs3732408	0.81[EUR][1000 genomes]
rs3772128	0.95[CEU][hapmap]
rs3772130	0.96[CEU][hapmap]
rs3805127	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4280673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4311252	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413346	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55657471	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57636696	0.84[AMR][1000 genomes]
rs6769102	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6776670	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780302	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784571	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629369	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7649092	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9289177	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812137	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812228	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816844	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9822949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825248	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9826473	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9839617	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841595	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848027	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856641	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9878086	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883467	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
2	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
3	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
4	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
5	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
6	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
7	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
8	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	8 gene(s)	inside rSNPs	diseases
9	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6768621	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs6768621	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs6768621	HCLS1	cis	Whole Blood	GTEx
rs6768621	IQCB1	cis	Whole Blood	GTEx
rs6768621	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:121491600-121552600	Weak transcription	NHLF	lung
3	chr3:121494200-121544200	Weak transcription	Fetal Brain Male	brain
4	chr3:121500200-121541400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:121507000-121545400	Weak transcription	Fetal Heart	heart
6	chr3:121507200-121536000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:121508200-121535800	Weak transcription	Psoas Muscle	Psoas
8	chr3:121508400-121536400	Weak transcription	HUVEC	blood vessel
9	chr3:121508600-121541400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:121519600-121530400	Weak transcription	Right Ventricle	heart
11	chr3:121521600-121531600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:121521800-121531600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:121522000-121531200	Strong transcription	Dnd41	blood
14	chr3:121522200-121531200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:121522400-121536600	Weak transcription	Fetal Kidney	kidney
16	chr3:121523000-121531600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:121523200-121531200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:121523200-121534000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:121524400-121536600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:121524600-121536400	Weak transcription	K562	blood
21	chr3:121524800-121541400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:121525200-121536400	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:121525400-121530600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:121526000-121542800	Weak transcription	NH-A	brain
25	chr3:121526200-121540000	Weak transcription	NHDF-Ad	bronchial
26	chr3:121526400-121530400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:121526400-121533600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:121526400-121536400	Weak transcription	Osteobl	bone
29	chr3:121526800-121531600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:121527600-121531000	Strong transcription	Fetal Thymus	thymus
31	chr3:121527800-121536400	Weak transcription	A549	lung
32	chr3:121528000-121553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:121528200-121530400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:121528200-121530600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:121528200-121531200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:121528200-121531200	Strong transcription	Brain Angular Gyrus	brain
37	chr3:121528200-121531400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:121528400-121531000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:121528400-121531200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:121528400-121531400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:121528600-121530600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:121528600-121532000	Strong transcription	Primary T cells from cord blood	blood
43	chr3:121528600-121536000	Weak transcription	HSMM	muscle
44	chr3:121528600-121537200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:121528800-121530800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr3:121528800-121531400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:121528800-121531400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:121529000-121531000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr3:121529000-121531600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:121529000-121531800	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links