Variant report

Variant	rs6771728
Chromosome Location	chr3:156263097-156263098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156262516..156264945-chr3:156391485..156393520,2	MCF-7	breast:
2	chr3:156260735..156275674-chr3:156389736..156397850,44	K562	blood:
3	chr3:156261650..156264096-chr3:156875921..156878596,2	MCF-7	breast:
4	chr3:156261351..156264405-chr3:156391990..156397346,7	K562	blood:
5	chr3:156259529..156263579-chr3:156391738..156394703,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10936027	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11710396	0.90[ASN][1000 genomes]
rs13065924	1.00[JPT][hapmap]
rs13068904	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083246	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13088140	1.00[JPT][hapmap]
rs17354147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2874390	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3773713	1.00[JPT][hapmap]
rs3773717	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773719	1.00[ASN][1000 genomes]
rs6441074	1.00[JPT][hapmap]
rs6441075	1.00[JPT][hapmap]
rs6441076	1.00[JPT][hapmap]
rs6764265	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764992	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71310479	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71310481	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619602	1.00[JPT][hapmap]
rs8665	1.00[JPT][hapmap]
rs9837799	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917691	1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6771728	SSR3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156246800-156263600	Weak transcription	Fetal Brain Female	brain
2	chr3:156247200-156263800	Weak transcription	Thymus	Thymus
3	chr3:156249000-156264600	Weak transcription	Brain Germinal Matrix	brain
4	chr3:156252000-156263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:156252000-156270200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:156252200-156268600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:156253400-156268200	Weak transcription	Gastric	stomach
8	chr3:156253600-156268200	Weak transcription	Small Intestine	intestine
9	chr3:156253600-156271400	Weak transcription	Stomach Mucosa	stomach
10	chr3:156253800-156270800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:156254200-156270200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:156254600-156265400	Strong transcription	Liver	Liver
13	chr3:156255200-156268600	Strong transcription	Dnd41	blood
14	chr3:156255200-156270600	Strong transcription	A549	lung
15	chr3:156255600-156263200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:156255600-156270800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:156255800-156270200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:156255800-156270200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:156255800-156270600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:156255800-156270800	Strong transcription	Fetal Intestine Large	intestine
21	chr3:156256000-156268600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:156256200-156263800	Strong transcription	NHEK	skin
23	chr3:156256200-156264400	Strong transcription	HMEC	breast
24	chr3:156256200-156270400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:156256200-156270400	Strong transcription	Primary hematopoietic stem cells	blood
26	chr3:156256400-156264600	Strong transcription	K562	blood
27	chr3:156256400-156270400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:156256600-156267200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:156256600-156267400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:156256600-156270600	Strong transcription	Primary B cells from cord blood	blood
31	chr3:156256800-156264400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:156256800-156264400	Strong transcription	GM12878-XiMat	blood
33	chr3:156256800-156266800	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:156256800-156269400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:156256800-156269600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:156256800-156270600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:156256800-156271000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:156257000-156263200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:156257000-156265600	Strong transcription	NHLF	lung
40	chr3:156257000-156269600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:156257000-156270400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:156257000-156270600	Strong transcription	Fetal Thymus	thymus
43	chr3:156257000-156271000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:156257000-156271200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr3:156257200-156269600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:156257200-156270200	Strong transcription	Hela-S3	cervix
47	chr3:156257600-156264800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:156257800-156263600	Weak transcription	Spleen	Spleen
49	chr3:156257800-156263600	Strong transcription	HSMMtube	muscle
50	chr3:156257800-156266000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links