Variant report

Variant	rs9390235
Chromosome Location	chr6:145168455-145168456
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:145166979..145168602-chr6:145169324..145170941,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10192	0.92[JPT][hapmap]
rs1111807	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1111808	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17074328	0.88[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2297847	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4321838	0.89[EUR][1000 genomes]
rs55704038	0.91[EUR][1000 genomes]
rs58797562	0.92[EUR][1000 genomes]
rs6903007	0.88[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6925712	0.90[EUR][1000 genomes]
rs73596379	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73596388	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73596396	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73598008	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73604356	0.97[EUR][1000 genomes]
rs73606408	0.94[EUR][1000 genomes]
rs7747041	0.88[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7748226	0.83[JPT][hapmap]
rs7755539	0.92[JPT][hapmap]
rs9386085	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399503	0.93[JPT][hapmap]
rs9403611	0.92[JPT][hapmap]
rs9403617	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv886740	chr6:145105354-145199259	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145116400-145169000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:145117400-145175200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr6:145126600-145169400	Weak transcription	Stomach Mucosa	stomach
4	chr6:145130800-145172200	Weak transcription	NH-A	brain
5	chr6:145137400-145176800	Weak transcription	Fetal Heart	heart
6	chr6:145137800-145175800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:145141400-145172000	Weak transcription	Brain Substantia Nigra	brain
8	chr6:145141400-145175200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:145142000-145171400	Weak transcription	HMEC	breast
10	chr6:145143000-145173600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr6:145154200-145175200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:145154400-145173400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr6:145154400-145175000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:145154400-145175200	Strong transcription	Dnd41	blood
15	chr6:145154800-145169200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:145154800-145175200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr6:145155800-145171800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:145156600-145168600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:145157400-145173400	Weak transcription	Fetal Brain Male	brain
20	chr6:145157800-145169200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:145157800-145176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:145158600-145176800	Weak transcription	Esophagus	oesophagus
23	chr6:145158800-145173600	Weak transcription	Psoas Muscle	Psoas
24	chr6:145158800-145174800	Weak transcription	Placenta	Placenta
25	chr6:145159200-145173800	Weak transcription	GM12878-XiMat	blood
26	chr6:145159200-145176600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:145159400-145168600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:145159400-145168800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:145159400-145171600	Weak transcription	Fetal Kidney	kidney
30	chr6:145159400-145177400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:145159600-145175200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:145161000-145170000	Weak transcription	Aorta	Aorta
33	chr6:145161000-145174400	Weak transcription	Right Ventricle	heart
34	chr6:145161000-145176000	Weak transcription	Pancreas	Pancrea
35	chr6:145161000-145179000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:145162000-145169000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:145162200-145170800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:145162200-145171600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:145162400-145168600	Weak transcription	Fetal Lung	lung
40	chr6:145162400-145172400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:145162400-145173200	Weak transcription	Colonic Mucosa	Colon
42	chr6:145162600-145169400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:145162600-145169600	Weak transcription	Brain Anterior Caudate	brain
44	chr6:145162600-145171200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:145162600-145173800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:145162600-145176400	Weak transcription	Fetal Intestine Large	intestine
47	chr6:145162800-145176600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:145163200-145169200	Weak transcription	Ovary	ovary
49	chr6:145163800-145176200	Weak transcription	Fetal Intestine Small	intestine
50	chr6:145164200-145174800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links