Variant report

Variant	rs6764992
Chromosome Location	chr3:156259178-156259179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155868368..155868971-chr3:156258538..156259204,2	K562	blood:
2	chr3:156257972..156262357-chr3:156268019..156272928,6	MCF-7	breast:
3	chr3:156257682..156260164-chr3:156541175..156543655,2	MCF-7	breast:
4	chr3:156244452..156246713-chr3:156259081..156262039,2	K562	blood:

Variant related genes	Relation type
ENSG00000197980	Chromatin interaction
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10936027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710396	0.87[ASN][1000 genomes]
rs12107507	1.00[YRI][hapmap]
rs13065924	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13068904	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088140	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17354147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2874390	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3773717	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773719	0.96[ASN][1000 genomes]
rs6441074	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6441075	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6441076	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6764265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771728	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802811	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71310479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71310481	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs756335	0.90[CEU][hapmap]
rs7619602	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs8665	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9837799	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9917691	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877683	chr3:156180366-156272351	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6764992	SSR3	cis	lymphoblastoid	seeQTL
rs6764992	SSR3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156240400-156260200	Weak transcription	Esophagus	oesophagus
2	chr3:156246800-156263600	Weak transcription	Fetal Brain Female	brain
3	chr3:156247200-156263800	Weak transcription	Thymus	Thymus
4	chr3:156249000-156264600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:156251600-156259200	Weak transcription	Ovary	ovary
6	chr3:156252000-156263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:156252000-156270200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:156252200-156268600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:156253000-156259200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:156253400-156260800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:156253400-156268200	Weak transcription	Gastric	stomach
12	chr3:156253600-156260200	Weak transcription	Fetal Stomach	stomach
13	chr3:156253600-156268200	Weak transcription	Small Intestine	intestine
14	chr3:156253600-156271400	Weak transcription	Stomach Mucosa	stomach
15	chr3:156253800-156259400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:156253800-156259800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:156253800-156260000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:156253800-156260000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:156253800-156260800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:156253800-156260800	Weak transcription	Right Ventricle	heart
21	chr3:156253800-156261200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:156253800-156261400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:156253800-156270800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:156254000-156259400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:156254000-156259800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:156254000-156260000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:156254000-156260000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:156254200-156270200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:156254600-156259200	Weak transcription	Placenta	Placenta
30	chr3:156254600-156260200	Weak transcription	Fetal Heart	heart
31	chr3:156254600-156265400	Strong transcription	Liver	Liver
32	chr3:156255200-156268600	Strong transcription	Dnd41	blood
33	chr3:156255200-156270600	Strong transcription	A549	lung
34	chr3:156255600-156259600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:156255600-156259800	Strong transcription	HUVEC	blood vessel
36	chr3:156255600-156261200	Strong transcription	NHDF-Ad	bronchial
37	chr3:156255600-156261400	Strong transcription	Osteobl	bone
38	chr3:156255600-156263200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:156255600-156270800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:156255800-156260000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:156255800-156261200	Weak transcription	Brain Anterior Caudate	brain
42	chr3:156255800-156270200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:156255800-156270200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:156255800-156270600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr3:156255800-156270800	Strong transcription	Fetal Intestine Large	intestine
46	chr3:156256000-156268600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:156256200-156259200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:156256200-156260000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:156256200-156263800	Strong transcription	NHEK	skin
50	chr3:156256200-156264400	Strong transcription	HMEC	breast

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