Variant report

Variant	rs1746471
Chromosome Location	chr6:131504851-131504852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131504234..131504890-chr8:67976530..67977471,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104218	Chromatin interaction
ENSG00000121022	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11154621	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11154622	1.00[CHB][hapmap]
rs11755717	1.00[CHB][hapmap]
rs11758994	1.00[CHB][hapmap]
rs1190788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190796	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190800	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190802	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1190805	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1190806	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1190809	0.87[EUR][1000 genomes]
rs1190810	0.94[EUR][1000 genomes]
rs1190812	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1209159	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195700	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap]
rs13200165	1.00[CHB][hapmap]
rs13206776	1.00[CHB][hapmap]
rs1570348	1.00[CHB][hapmap]
rs1729549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746469	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs1746470	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1746474	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17573187	1.00[CHB][hapmap]
rs17651753	1.00[CHB][hapmap]
rs17787964	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1885641	1.00[CHB][hapmap]
rs3777474	0.91[EUR][1000 genomes]
rs3777476	1.00[CHB][hapmap]
rs3777487	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3903759	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs4310080	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs4424112	1.00[CHB][hapmap]
rs56318353	1.00[ASN][1000 genomes]
rs66533103	0.80[EUR][1000 genomes]
rs7743894	1.00[CHB][hapmap]
rs9492861	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs9492864	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs9492865	1.00[CHB][hapmap]
rs9492869	1.00[CHB][hapmap]
rs9492874	0.83[ASN][1000 genomes]
rs9492883	1.00[CHB][hapmap]

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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' 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:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131457600-131505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:131457600-131520800	Weak transcription	Right Ventricle	heart
3	chr6:131458000-131505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:131458000-131505800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:131458200-131505200	Weak transcription	Fetal Lung	lung
6	chr6:131458200-131513400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:131483000-131506200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:131484400-131509200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:131485400-131509600	Weak transcription	Small Intestine	intestine
10	chr6:131485600-131514000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:131486000-131505000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:131486000-131505600	Weak transcription	HepG2	liver
13	chr6:131486200-131505800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:131486400-131505000	Weak transcription	Placenta	Placenta
15	chr6:131487000-131505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:131487000-131512800	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:131488200-131534800	Weak transcription	Gastric	stomach
18	chr6:131489000-131513000	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:131491200-131508000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:131493800-131506600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:131494200-131505200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:131494800-131514000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:131496600-131507200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:131497400-131505200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:131499200-131506000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:131500000-131505600	Weak transcription	Esophagus	oesophagus
27	chr6:131500200-131505600	Weak transcription	Ovary	ovary
28	chr6:131501400-131505000	Weak transcription	Lung	lung
29	chr6:131501400-131505400	Weak transcription	Left Ventricle	heart
30	chr6:131503200-131505000	Weak transcription	Adipose Nuclei	Adipose
31	chr6:131503600-131505200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:131504000-131505000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:131504200-131505000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr6:131504200-131505000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr6:131504200-131505000	Enhancers	Primary B cells from cord blood	blood
36	chr6:131504200-131505000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr6:131504200-131505000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:131504200-131505000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr6:131504200-131505000	Enhancers	Fetal Muscle Trunk	muscle
40	chr6:131504200-131505000	Enhancers	Fetal Thymus	thymus
41	chr6:131504200-131505000	Enhancers	Pancreas	Pancrea
42	chr6:131504200-131505200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr6:131504200-131505200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr6:131504200-131505200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:131504200-131505200	Enhancers	Primary T cells from cord blood	blood
46	chr6:131504200-131505200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr6:131504200-131505200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:131504200-131505200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr6:131504200-131505200	Enhancers	Dnd41	blood
50	chr6:131504200-131514000	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links