Variant report

Variant	rs6778324
Chromosome Location	chr3:45971022-45971023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:45829160..45831402-chr3:45969746..45971522,2	K562	blood:
2	chr3:45969350..45971618-chr3:45977990..45979825,2	MCF-7	breast:
3	chr3:45970697..45972556-chr3:46017144..46019977,2	K562	blood:
4	chr3:45802267..45803322-chr3:45970211..45971183,11	K562	blood:
5	chr3:45881689..45884570-chr3:45968593..45971542,2	MCF-7	breast:
6	chr3:45970536..45971214-chr3:46120157..46120881,2	MCF-7	breast:
7	chr3:45965599..45968442-chr3:45968731..45971652,2	K562	blood:

Variant related genes	Relation type
ENSG00000163818	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1072755	0.81[ASN][1000 genomes]
rs17078449	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17078454	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2234351	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35537559	0.85[EUR][1000 genomes]
rs3774638	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774640	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796376	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3821883	0.85[EUR][1000 genomes]
rs4683152	0.80[ASN][1000 genomes]
rs4683153	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs57204020	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59226168	0.83[EUR][1000 genomes]
rs59767267	0.83[EUR][1000 genomes]
rs60237998	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60779624	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62242787	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62242788	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62242796	0.85[EUR][1000 genomes]
rs62245106	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62245108	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6778225	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781121	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6781668	0.85[EUR][1000 genomes]
rs6800954	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7631809	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs936939	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:45958400-45974200	Strong transcription	Fetal Stomach	stomach
4	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
7	chr3:45959000-45973600	Weak transcription	Fetal Kidney	kidney
8	chr3:45959200-45979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:45959400-45971800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:45959400-45973400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:45959600-45973200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:45959800-45974600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:45959800-45979800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:45959800-45979800	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:45959800-45980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:45960000-45979400	Strong transcription	Fetal Intestine Large	intestine
19	chr3:45960000-45980400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:45960200-45974200	Strong transcription	Fetal Intestine Small	intestine
21	chr3:45960400-45980200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:45961600-45979400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:45961600-45979800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:45963800-45979800	Strong transcription	Primary T cells from cord blood	blood
26	chr3:45963800-45979800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:45964400-45980400	Weak transcription	Fetal Brain Female	brain
28	chr3:45965200-45972200	Weak transcription	Brain Germinal Matrix	brain
29	chr3:45965400-45971400	Weak transcription	NHEK	skin
30	chr3:45965400-45975800	Weak transcription	Psoas Muscle	Psoas
31	chr3:45965400-45977600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:45965400-45980400	Weak transcription	Fetal Brain Male	brain
33	chr3:45965600-45971200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:45965800-45972000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:45965800-45972400	Weak transcription	HSMMtube	muscle
36	chr3:45966000-45971800	Weak transcription	Hela-S3	cervix
37	chr3:45966000-45980600	Weak transcription	HMEC	breast
38	chr3:45966200-45974000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:45966800-45979600	Strong transcription	Liver	Liver
40	chr3:45967000-45976600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:45967000-45978200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr3:45967200-45974600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr3:45967200-45977600	Strong transcription	Primary B cells from cord blood	blood
44	chr3:45967200-45979400	Strong transcription	Adipose Nuclei	Adipose
45	chr3:45967200-45979800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:45967200-45980000	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:45967400-45971400	Weak transcription	Stomach Mucosa	stomach
48	chr3:45967400-45979800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:45967800-45976200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:45968000-45974000	Strong transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links