Variant report

Variant	rs6474820
Chromosome Location	chr9:14142907-14142908
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	chr9:14137259..14139020-chr9:14141233..14143337,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10511592	0.82[JPT][hapmap]
rs12552654	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs12554151	0.93[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13300925	0.85[JPT][hapmap]
rs16931403	0.81[JPT][hapmap]
rs2382437	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2382438	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2382439	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2382440	0.92[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2382443	0.82[CHB][hapmap]
rs4237133	0.92[CEU][hapmap]
rs7028001	0.85[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs7029562	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7030475	0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7031735	0.83[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs7042127	0.84[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7042365	0.85[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs7045411	0.84[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs723968	0.81[JPT][hapmap]
rs73642096	0.81[ASN][1000 genomes]
rs7863447	0.84[CEU][hapmap]
rs7868947	0.84[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats 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	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh 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	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv892595	chr9:14129951-14168029	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14108800-14143800	Weak transcription	Fetal Intestine Small	intestine
2	chr9:14116600-14159200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:14116600-14179200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:14116800-14156000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:14117000-14171200	Weak transcription	Hela-S3	cervix
6	chr9:14120200-14159000	Weak transcription	NHLF	lung
7	chr9:14120600-14151600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:14120600-14154800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr9:14120600-14159000	Weak transcription	NH-A	brain
10	chr9:14121600-14143600	Weak transcription	Brain Substantia Nigra	brain
11	chr9:14123800-14198600	Weak transcription	Gastric	stomach
12	chr9:14126400-14148200	Weak transcription	Placenta	Placenta
13	chr9:14126800-14144800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr9:14127000-14146000	Weak transcription	Osteobl	bone
15	chr9:14127000-14151200	Weak transcription	Aorta	Aorta
16	chr9:14127000-14156400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:14131800-14173200	Weak transcription	Pancreas	Pancrea
18	chr9:14132000-14144600	Weak transcription	Fetal Brain Female	brain
19	chr9:14133000-14144800	Weak transcription	Left Ventricle	heart
20	chr9:14133400-14153200	Weak transcription	Psoas Muscle	Psoas
21	chr9:14133800-14143800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:14133800-14146000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:14133800-14146200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:14134000-14148000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:14134000-14151000	Weak transcription	Adipose Nuclei	Adipose
26	chr9:14134000-14181000	Weak transcription	Ovary	ovary
27	chr9:14134200-14143400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:14134200-14144400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:14134200-14144600	Weak transcription	Fetal Heart	heart
30	chr9:14134200-14145600	Weak transcription	Liver	Liver
31	chr9:14134200-14156200	Weak transcription	Right Ventricle	heart
32	chr9:14134200-14159400	Weak transcription	Fetal Stomach	stomach
33	chr9:14136000-14155000	Weak transcription	Brain Germinal Matrix	brain
34	chr9:14137200-14146200	Weak transcription	A549	lung
35	chr9:14137400-14143200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:14137400-14144200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:14137400-14145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:14137600-14143200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr9:14137600-14148200	Weak transcription	NHEK	skin
40	chr9:14137600-14153400	Weak transcription	HMEC	breast
41	chr9:14140200-14143800	Weak transcription	Colon Smooth Muscle	Colon
42	chr9:14140200-14148000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:14140400-14144400	Weak transcription	HSMM	muscle
44	chr9:14140400-14147200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:14140600-14143000	Strong transcription	HUVEC	blood vessel
46	chr9:14141000-14144800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:14141200-14144800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:14141200-14144800	Weak transcription	Fetal Muscle Leg	muscle
49	chr9:14141800-14143000	Strong transcription	Fetal Lung	lung
50	chr9:14142200-14159000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links