Variant report

Variant	rs10259964
Chromosome Location	chr7:101535924-101535925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101446447..101448441-chr7:101533510..101536360,2	MCF-7	breast:
2	chr7:101528188..101530830-chr7:101535885..101537732,3	K562	blood:
3	chr7:101532182..101534977-chr7:101535294..101537125,2	K562	blood:
4	chr7:101534339..101537271-chr7:101538707..101540826,3	K562	blood:
5	chr7:101534473..101537289-chr7:101541680..101543793,2	K562	blood:
6	chr7:101535565..101538438-chr7:101544906..101547711,2	K562	blood:
7	chr7:101535633..101539111-chr7:101541192..101544235,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10081174	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10226289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10240601	0.92[EUR][1000 genomes]
rs10241905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10242019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10261524	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264855	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271171	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10271838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532535	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12534641	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12539310	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs13227531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229243	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13236072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13241079	0.82[ASN][1000 genomes]
rs13241252	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2410921	0.89[ASN][1000 genomes]
rs28409703	0.88[ASN][1000 genomes]
rs34750675	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35065711	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4729756	0.80[ASN][1000 genomes]
rs4729759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55824493	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60656667	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72603509	0.84[AMR][1000 genomes]
rs72603510	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72603511	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72603512	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9656073	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101523200-101543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:101526000-101540400	Weak transcription	Aorta	Aorta
3	chr7:101526200-101536800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:101526400-101542200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:101526800-101543000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:101527000-101538600	Weak transcription	Fetal Muscle Leg	muscle
7	chr7:101527000-101543000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:101527000-101543000	Weak transcription	NHEK	skin
9	chr7:101527200-101542200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:101528000-101536400	Weak transcription	K562	blood
11	chr7:101528200-101539600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:101528600-101555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:101528800-101538600	Weak transcription	Dnd41	blood
14	chr7:101528800-101544000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:101529400-101539000	Weak transcription	Thymus	Thymus
16	chr7:101529400-101539400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:101529400-101539600	Weak transcription	Fetal Heart	heart
18	chr7:101529400-101543000	Weak transcription	Brain Substantia Nigra	brain
19	chr7:101529400-101554200	Weak transcription	Primary T cells from cord blood	blood
20	chr7:101530200-101538800	Weak transcription	Fetal Thymus	thymus
21	chr7:101530200-101539600	Weak transcription	Pancreas	Pancrea
22	chr7:101530400-101539400	Weak transcription	Lung	lung
23	chr7:101530600-101539400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr7:101530600-101559800	Weak transcription	GM12878-XiMat	blood
25	chr7:101531000-101545000	Weak transcription	Gastric	stomach
26	chr7:101531000-101548000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:101531400-101539400	Weak transcription	Fetal Stomach	stomach
28	chr7:101531400-101543000	Weak transcription	Placenta	Placenta
29	chr7:101531400-101554600	Weak transcription	Hela-S3	cervix
30	chr7:101532400-101536800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr7:101532400-101536800	Weak transcription	Stomach Mucosa	stomach
32	chr7:101532800-101536400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr7:101533400-101536600	Weak transcription	Ovary	ovary
34	chr7:101533600-101536600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr7:101533600-101536600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:101533600-101536600	Weak transcription	Fetal Intestine Small	intestine
37	chr7:101533600-101539800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:101533800-101538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:101533800-101539400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr7:101533800-101559000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr7:101534200-101537000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr7:101534200-101539600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:101534200-101546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr7:101534400-101537000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr7:101534400-101539400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:101534600-101536000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr7:101534600-101536200	Enhancers	Brain Germinal Matrix	brain
48	chr7:101534600-101536200	Bivalent Enhancer	Fetal Brain Male	brain
49	chr7:101534600-101536400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:101534800-101537000	Enhancers	Fetal Brain Female	brain

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