Variant report

Variant	rs4647421
Chromosome Location	chr9:98009017-98009018
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98007562..98009225-chr9:98010300..98012768,2	MCF-7	breast:
2	chr9:98003959..98008531-chr9:98008535..98011761,4	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10283758	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993475	0.87[EUR][1000 genomes]
rs10993479	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10993483	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10993503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993520	0.83[AMR][1000 genomes]
rs1105979	0.84[AMR][1000 genomes]
rs12337959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12338907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12339700	0.84[AMR][1000 genomes]
rs12342782	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12344626	0.82[EUR][1000 genomes]
rs12350646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12352586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12377946	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17679141	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1886992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1889241	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs28626189	0.84[EUR][1000 genomes]
rs28658564	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs356659	0.86[TSI][hapmap]
rs4237226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647372	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647373	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647401	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647441	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743990	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4744443	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4744444	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4744457	0.84[AMR][1000 genomes]
rs4744458	0.83[AMR][1000 genomes]
rs554879	0.82[TSI][hapmap]
rs56134407	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62560523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62560524	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs640628	0.82[TSI][hapmap]
rs7357617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs879559	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97973600-98024000	Weak transcription	Gastric	stomach
2	chr9:97974000-98009400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:97981400-98012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:97983400-98012400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:97987200-98015400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:97988400-98012200	Weak transcription	Fetal Kidney	kidney
7	chr9:97989200-98009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:97989200-98012400	Weak transcription	Ovary	ovary
9	chr9:97989400-98012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:97989400-98013400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:97989600-98012200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:97989800-98011200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:97990200-98013400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr9:97990400-98012600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:97991000-98010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr9:97991200-98024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:97992600-98013400	Weak transcription	Liver	Liver
18	chr9:97994200-98011400	Weak transcription	Hela-S3	cervix
19	chr9:97994800-98011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr9:97994800-98017200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr9:97995400-98012800	Weak transcription	HSMM	muscle
22	chr9:97996400-98012400	Weak transcription	Psoas Muscle	Psoas
23	chr9:97996800-98012800	Weak transcription	HSMMtube	muscle
24	chr9:97997600-98012400	Weak transcription	Fetal Brain Male	brain
25	chr9:97999800-98019000	Weak transcription	Aorta	Aorta
26	chr9:98001200-98012400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:98002400-98015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:98002600-98012400	Weak transcription	Esophagus	oesophagus
29	chr9:98004000-98011200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr9:98004800-98012200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:98005200-98012400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:98005400-98012400	Weak transcription	Fetal Thymus	thymus
33	chr9:98005400-98013000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:98005600-98012400	Weak transcription	Colon Smooth Muscle	Colon
35	chr9:98005600-98012400	Weak transcription	HepG2	liver
36	chr9:98006000-98016800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:98006200-98009600	Strong transcription	Fetal Intestine Large	intestine
38	chr9:98006200-98009600	Strong transcription	Fetal Muscle Leg	muscle
39	chr9:98006400-98009200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr9:98007000-98012400	Weak transcription	Brain Germinal Matrix	brain
41	chr9:98007000-98013200	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:98007200-98009200	Strong transcription	Fetal Lung	lung
43	chr9:98007200-98009400	Strong transcription	Primary T cells from cord blood	blood
44	chr9:98007200-98009600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:98007400-98009600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr9:98007400-98010000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr9:98007400-98024000	Weak transcription	Small Intestine	intestine
48	chr9:98007600-98011600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:98008000-98010400	Weak transcription	HUVEC	blood vessel
50	chr9:98008000-98011200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links