Variant report

Variant	rs9399456
Chromosome Location	chr6:144008361-144008362
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143996710..144001910-chr6:144005817..144014875,10	MCF-7	breast:
2	chr6:144005095..144007441-chr6:144008353..144010500,3	K562	blood:
3	chr6:144004544..144009046-chr6:144017005..144020189,4	K562	blood:
4	chr6:144002192..144005187-chr6:144008261..144010591,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11155318	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11155320	0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11962519	0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12530310	0.92[ASN][1000 genomes]
rs13190772	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs13191259	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13204954	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13220613	0.82[CHB][hapmap]
rs2024693	0.89[CEU][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2051008	0.85[ASN][1000 genomes]
rs2092762	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2474150	0.83[ASN][1000 genomes]
rs3924968	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4299843	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4523103	0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs6570571	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570572	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6570573	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913687	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6914940	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6916245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931556	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7450663	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7738179	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7740883	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7741628	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7741901	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7741998	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7747182	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7758298	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7760178	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762598	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7764549	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7766091	0.87[CHB][hapmap]
rs7766510	0.84[AFR][1000 genomes]
rs7770812	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7771214	1.00[CHB][hapmap]
rs7772898	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7773502	1.00[CHB][hapmap]
rs910419	0.95[CHB][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9321933	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9321934	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9321935	0.86[JPT][hapmap]
rs9376773	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9376774	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376775	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376777	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9390127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399454	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9399459	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403520	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403522	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9484794	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9496718	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9496721	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9496729	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9496733	1.00[CHB][hapmap]
rs9496734	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496735	0.88[ASN][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	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144000600-144008800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:144001800-144012200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:144002000-144008400	Weak transcription	Placenta	Placenta
4	chr6:144002000-144013000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr6:144002800-144011200	Weak transcription	Hela-S3	cervix
6	chr6:144003600-144009800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:144003600-144015000	Weak transcription	Esophagus	oesophagus
8	chr6:144003600-144015000	Weak transcription	Gastric	stomach
9	chr6:144003800-144008800	Weak transcription	Fetal Stomach	stomach
10	chr6:144004400-144010000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:144004400-144013000	Weak transcription	Fetal Kidney	kidney
12	chr6:144005000-144009000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:144005000-144020400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:144005600-144016000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:144005800-144009000	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:144005800-144015200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:144006000-144008600	Weak transcription	Fetal Lung	lung
18	chr6:144006000-144009000	Weak transcription	Right Ventricle	heart
19	chr6:144006000-144009800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:144006000-144011000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:144006000-144013200	Weak transcription	Small Intestine	intestine
22	chr6:144006000-144017800	Weak transcription	Fetal Heart	heart
23	chr6:144007600-144008400	Enhancers	Ovary	ovary
24	chr6:144007800-144008400	Enhancers	H9 Cell Line	embryonic stem cell
25	chr6:144007800-144008400	Enhancers	Fetal Intestine Large	intestine
26	chr6:144007800-144008600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:144007800-144008600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:144007800-144008600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:144007800-144008600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:144007800-144008600	Enhancers	NHLF	lung
31	chr6:144007800-144008800	Enhancers	NHEK	skin
32	chr6:144007800-144009000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:144007800-144009000	Enhancers	HSMM	muscle
34	chr6:144007800-144009200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr6:144007800-144009200	Enhancers	HMEC	breast
36	chr6:144007800-144009200	Enhancers	NH-A	brain
37	chr6:144007800-144009400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:144007800-144009400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr6:144007800-144009400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:144007800-144009600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr6:144007800-144009600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr6:144007800-144011800	Enhancers	Left Ventricle	heart
43	chr6:144007800-144013200	Enhancers	HepG2	liver
44	chr6:144007800-144013600	Enhancers	H1 Cell Line	embryonic stem cell
45	chr6:144008000-144008400	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr6:144008000-144008800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:144008000-144008800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:144008000-144008800	Enhancers	Adipose Nuclei	Adipose
49	chr6:144008000-144008800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr6:144008000-144008800	Weak transcription	Fetal Intestine Small	intestine

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