Variant report

Variant	rs6772519
Chromosome Location	chr3:99550321-99550322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99543572..99547778-chr3:99548143..99551852,5	K562	blood:
2	chr3:99536894..99538407-chr3:99549555..99551120,2	K562	blood:
3	chr3:99548996..99551072-chr3:99971519..99973531,2	MCF-7	breast:
4	chr3:99536004..99538111-chr3:99547976..99550657,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16841650	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs16841653	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs16841712	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs17313676	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs17314245	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs17314280	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs17392822	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs17778804	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2035400	1.00[YRI][hapmap]
rs41444055	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6762809	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6784150	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6787184	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6791426	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6805703	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6807615	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6808420	1.00[YRI][hapmap]
rs7611313	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7612083	1.00[YRI][hapmap]
rs7612089	1.00[YRI][hapmap]
rs7619738	1.00[YRI][hapmap]
rs7626214	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7626310	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs768527	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9756455	1.00[YRI][hapmap]
rs9824017	1.00[YRI][hapmap]
rs9843372	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99562600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
3	chr3:99537400-99551000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:99537400-99552400	Weak transcription	Ovary	ovary
5	chr3:99537800-99552400	Weak transcription	Pancreas	Pancrea
6	chr3:99537800-99561800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:99537800-99562400	Weak transcription	Left Ventricle	heart
8	chr3:99538000-99550400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:99538000-99550800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:99538000-99552000	Weak transcription	Fetal Intestine Small	intestine
11	chr3:99538000-99552400	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:99538000-99556000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:99538000-99556800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:99538000-99563600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:99538200-99550800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:99538200-99555400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
18	chr3:99538400-99550800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:99538400-99551000	Weak transcription	Primary B cells from cord blood	blood
20	chr3:99540200-99550600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:99540800-99552000	Weak transcription	GM12878-XiMat	blood
22	chr3:99541200-99550400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:99543000-99551000	Weak transcription	Small Intestine	intestine
24	chr3:99543000-99557200	Weak transcription	Psoas Muscle	Psoas
25	chr3:99543000-99562600	Weak transcription	Placenta	Placenta
26	chr3:99544200-99550600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:99544200-99550800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:99544200-99561800	Weak transcription	NHLF	lung
29	chr3:99544200-99564800	Weak transcription	K562	blood
30	chr3:99544400-99554400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:99544400-99557800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:99544400-99561800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:99544400-99561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:99544800-99558000	Weak transcription	NHEK	skin
35	chr3:99545000-99557800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:99545000-99558000	Weak transcription	HMEC	breast
37	chr3:99545000-99562000	Weak transcription	HSMM	muscle
38	chr3:99545400-99552200	Weak transcription	Fetal Stomach	stomach
39	chr3:99545600-99551000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:99547800-99550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:99548000-99552600	Weak transcription	Aorta	Aorta
42	chr3:99548600-99550600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:99549400-99552400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:99549400-99556800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:99549600-99551800	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links