Variant report

Variant	rs6799320
Chromosome Location	chr3:135802439-135802440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135800963..135802947-chr3:135914526..135916978,2	MCF-7	breast:
2	chr3:135793213..135794869-chr3:135799628..135802469,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10048942	0.84[CEU][hapmap]
rs10222451	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512990	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12330335	0.90[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12695644	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13068210	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13079205	0.90[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081671	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13082532	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13321220	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1393786	0.90[CEU][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1393787	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1403763	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs28509770	0.81[EUR][1000 genomes]
rs28519617	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28535121	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28669017	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34864445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35320690	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35352346	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3905668	0.81[EUR][1000 genomes]
rs56398805	0.81[EUR][1000 genomes]
rs6439629	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67109185	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67589653	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767060	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6769762	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6775778	0.84[CEU][hapmap]
rs6786582	0.90[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6792630	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793835	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799056	0.84[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6799517	0.81[EUR][1000 genomes]
rs9653930	0.90[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834966	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848926	0.90[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870122	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9881400	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS 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	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135771200-135809600	Weak transcription	Gastric	stomach
2	chr3:135775000-135809600	Weak transcription	Fetal Brain Male	brain
3	chr3:135775000-135809600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:135781400-135803000	Weak transcription	Right Ventricle	heart
5	chr3:135784200-135805600	Weak transcription	Stomach Mucosa	stomach
6	chr3:135790200-135802800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:135790200-135830800	Weak transcription	Psoas Muscle	Psoas
8	chr3:135790600-135809600	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:135790800-135802600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:135790800-135803000	Weak transcription	NHEK	skin
11	chr3:135790800-135807000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:135790800-135809400	Weak transcription	Adipose Nuclei	Adipose
13	chr3:135790800-135809600	Weak transcription	Aorta	Aorta
14	chr3:135790800-135809600	Weak transcription	Brain Angular Gyrus	brain
15	chr3:135790800-135809600	Weak transcription	Brain Anterior Caudate	brain
16	chr3:135790800-135809600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:135790800-135809600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:135791200-135802800	Weak transcription	HMEC	breast
19	chr3:135794400-135806600	Weak transcription	Fetal Heart	heart
20	chr3:135794400-135809600	Weak transcription	NH-A	brain
21	chr3:135795000-135803000	Weak transcription	NHLF	lung
22	chr3:135795200-135802800	Weak transcription	HSMMtube	muscle
23	chr3:135796000-135802800	Weak transcription	Lung	lung
24	chr3:135796600-135802800	Weak transcription	Fetal Brain Female	brain
25	chr3:135798200-135802600	Weak transcription	Liver	Liver
26	chr3:135798200-135809400	Weak transcription	Brain Substantia Nigra	brain
27	chr3:135798600-135804600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:135798600-135805800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:135798800-135803600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:135799400-135802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:135799600-135806600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:135800000-135805200	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:135800000-135805600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:135800400-135808000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:135800400-135815400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:135800600-135808400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:135800800-135802600	Strong transcription	Placenta	Placenta
38	chr3:135800800-135802800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:135800800-135802800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:135800800-135802800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:135800800-135802800	Strong transcription	Fetal Intestine Large	intestine
42	chr3:135800800-135803800	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:135800800-135805000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:135801000-135804600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr3:135801200-135802600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:135801400-135802600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:135801400-135803800	Strong transcription	Osteobl	bone
48	chr3:135801600-135803800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:135801600-135804200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:135801600-135805000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links