Variant report

Variant	rs10948811
Chromosome Location	chr6:13641739-13641740
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13622245..13624613-chr6:13641011..13644598,3	K562	blood:
2	chr6:13612104..13613937-chr6:13641245..13643744,2	K562	blood:
3	chr6:13634378..13636640-chr6:13639918..13642651,2	MCF-7	breast:
4	chr6:13614016..13617291-chr6:13638337..13642167,4	K562	blood:
5	chr6:13638375..13640882-chr6:13640960..13643091,4	K562	blood:
6	chr6:13639950..13644495-chr6:13710615..13714647,5	MCF-7	breast:
7	chr6:13641445..13646183-chr6:13647166..13651436,6	K562	blood:

Variant related genes	Relation type
ENSG00000225921	Chromatin interaction
ENSG00000010017	Chromatin interaction
ENSG00000261071	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10484251	0.84[CHB][hapmap]
rs10807467	0.92[YRI][hapmap]
rs10948804	0.96[YRI][hapmap]
rs11753232	0.84[CHB][hapmap]
rs11755634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11759518	0.84[CHB][hapmap]
rs11962124	0.93[YRI][hapmap]
rs11970591	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1362519	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1362520	0.92[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1573702	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080415	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237092	0.92[CEU][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2299026	0.82[CHB][hapmap]
rs2299027	0.84[CHB][hapmap]
rs2841514	0.92[YRI][hapmap]
rs2841517	0.92[YRI][hapmap]
rs3757260	0.93[YRI][hapmap]
rs3800503	0.92[YRI][hapmap]
rs3846912	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3906327	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715455	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715512	0.84[CHB][hapmap]
rs59120082	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6458997	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6459003	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6459020	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6459025	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6899402	0.89[YRI][hapmap]
rs6911121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915775	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6940759	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72829117	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72831038	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7741241	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744218	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475276	0.83[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1016744	chr6:13622143-13664028	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1019422	chr6:13622143-13694781	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1026597	chr6:13634669-13689882	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13617600-13642200	Strong transcription	Fetal Thymus	thymus
2	chr6:13617600-13642200	Strong transcription	HSMM	muscle
3	chr6:13617600-13642400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:13618000-13644200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:13618200-13641800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:13618200-13644400	Strong transcription	K562	blood
7	chr6:13618200-13661200	Weak transcription	Fetal Brain Male	brain
8	chr6:13620000-13647200	Strong transcription	Dnd41	blood
9	chr6:13620000-13649600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:13620400-13660400	Weak transcription	Pancreas	Pancrea
11	chr6:13620600-13691000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:13623600-13656200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:13625400-13660400	Weak transcription	Gastric	stomach
14	chr6:13625600-13642600	Weak transcription	A549	lung
15	chr6:13626000-13660400	Weak transcription	Lung	lung
16	chr6:13626600-13667800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:13626800-13669000	Weak transcription	Brain Anterior Caudate	brain
18	chr6:13631000-13642600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:13632000-13660400	Weak transcription	Psoas Muscle	Psoas
20	chr6:13632600-13656000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:13632800-13645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:13632800-13653800	Weak transcription	Hela-S3	cervix
23	chr6:13634000-13644600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr6:13634200-13642000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:13636400-13645000	Strong transcription	Placenta	Placenta
26	chr6:13636800-13652800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:13637200-13642200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:13637200-13642400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr6:13637200-13650600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:13637400-13644000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr6:13637400-13644400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:13637400-13645000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:13637400-13660400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:13637600-13641800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:13637600-13642600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:13637600-13644400	Strong transcription	Primary T cells from cord blood	blood
37	chr6:13637800-13645000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:13637800-13652400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:13638000-13661400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:13638800-13655000	Weak transcription	Fetal Kidney	kidney
41	chr6:13638800-13657000	Weak transcription	Fetal Heart	heart
42	chr6:13638800-13657800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:13638800-13657800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:13638800-13659400	Weak transcription	Brain Angular Gyrus	brain
45	chr6:13639000-13641800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:13639000-13643600	Weak transcription	GM12878-XiMat	blood
47	chr6:13639000-13652000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:13639000-13654800	Weak transcription	NHLF	lung
49	chr6:13639000-13660400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:13639000-13660600	Weak transcription	Colon Smooth Muscle	Colon

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