Variant report

Variant	rs7965539
Chromosome Location	chr12:46329564-46329565
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr12:46329260-46329567	T-47D	breast:	n/a	n/a
2	GATA3	chr12:46329305-46329600	T-47D	breast:	n/a	n/a
3	GATA3	chr12:46329247-46329645	T-47D	breast:	n/a	chr12:46329292-46329301

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46116634..46119081-chr12:46329014..46330818,2	K562	blood:

Variant related genes	Relation type
SCAF11	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10161062	1.00[YRI][hapmap]
rs10161510	0.86[YRI][hapmap]
rs10161536	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506264	0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10880858	1.00[YRI][hapmap]
rs11183248	0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574971	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12296933	1.00[YRI][hapmap]
rs12297214	0.84[YRI][hapmap]
rs12298184	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12302862	0.82[YRI][hapmap]
rs12307979	0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309988	1.00[YRI][hapmap]
rs12314576	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12316361	0.81[YRI][hapmap]
rs1549591	1.00[EUR][1000 genomes]
rs15852	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17096316	1.00[EUR][1000 genomes]
rs61009645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6582575	1.00[YRI][hapmap]
rs6582580	1.00[EUR][1000 genomes]
rs7133123	1.00[YRI][hapmap]
rs7296694	0.93[YRI][hapmap]
rs7303119	0.86[YRI][hapmap]
rs7304785	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7306774	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7308856	0.80[YRI][hapmap]
rs7308893	1.00[YRI][hapmap]
rs7309921	0.81[YRI][hapmap]
rs7310702	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081280	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081611	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7964495	0.86[YRI][hapmap]
rs7970212	1.00[EUR][1000 genomes]
rs7970367	1.00[EUR][1000 genomes]
rs7971936	1.00[EUR][1000 genomes]
rs7972499	0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7972650	0.85[YRI][hapmap]
rs7973967	0.87[YRI][hapmap]
rs7975170	0.80[YRI][hapmap]
rs7975408	1.00[YRI][hapmap]

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	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:46312000-46329800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:46312000-46330000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:46312000-46330000	Strong transcription	Primary B cells from peripheral blood	blood
5	chr12:46312200-46348600	Strong transcription	Dnd41	blood
6	chr12:46314600-46345600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:46316600-46343400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:46317000-46341400	Weak transcription	Gastric	stomach
9	chr12:46318800-46338600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:46318800-46339200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:46319200-46341400	Weak transcription	Lung	lung
12	chr12:46319200-46362800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:46321000-46333200	Weak transcription	Fetal Intestine Small	intestine
14	chr12:46322400-46337400	Weak transcription	Fetal Brain Female	brain
15	chr12:46322600-46331800	Weak transcription	Ovary	ovary
16	chr12:46322600-46335200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:46322600-46338600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:46322600-46340000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:46322600-46341400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:46322600-46341400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:46322600-46341400	Weak transcription	Pancreas	Pancrea
22	chr12:46322600-46360200	Weak transcription	Fetal Brain Male	brain
23	chr12:46322800-46338600	Weak transcription	Esophagus	oesophagus
24	chr12:46323200-46341400	Weak transcription	Colonic Mucosa	Colon
25	chr12:46323200-46341400	Weak transcription	Fetal Stomach	stomach
26	chr12:46323200-46341400	Weak transcription	Spleen	Spleen
27	chr12:46323600-46332000	Strong transcription	Primary B cells from cord blood	blood
28	chr12:46324200-46334600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:46324400-46351600	Weak transcription	Psoas Muscle	Psoas
30	chr12:46324600-46333600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:46324800-46331600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:46325000-46331600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:46325000-46331800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:46325000-46334400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:46325000-46335400	Weak transcription	Thymus	Thymus
36	chr12:46325000-46341400	Weak transcription	Left Ventricle	heart
37	chr12:46325200-46343400	Weak transcription	Right Ventricle	heart
38	chr12:46325600-46334600	Weak transcription	NHEK	skin
39	chr12:46325600-46334800	Weak transcription	Fetal Kidney	kidney
40	chr12:46325800-46331800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:46325800-46333600	Weak transcription	Fetal Lung	lung
42	chr12:46325800-46333800	Weak transcription	HMEC	breast
43	chr12:46326200-46334200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:46326200-46334600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:46326200-46335200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:46326200-46335400	Weak transcription	NHLF	lung
47	chr12:46326600-46333600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:46326600-46334000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:46326600-46334600	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:46326600-46338400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links