Variant report

Variant	rs556562
Chromosome Location	chr11:85666440-85666441
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85661662..85663622-chr11:85665077..85667243,2	K562	blood:
2	chr11:85664911..85667444-chr11:85667862..85673209,4	K562	blood:
3	chr11:85664784..85666650-chr11:85673268..85675684,2	K562	blood:
4	chr11:85664911..85667241-chr11:85670910..85673209,2	K562	blood:
5	chr11:85663607..85666587-chr11:86015226..86016933,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11234493	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1237230	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996108	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2077815	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2155051	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2458493	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2458496	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2458499	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2458500	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508688	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2508691	0.83[AFR][1000 genomes]
rs2509608	0.93[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2509609	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3016327	0.81[AMR][1000 genomes]
rs472618	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs488134	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs489486	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs493254	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs494369	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4944549	0.82[AMR][1000 genomes]
rs497711	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs504129	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs527162	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs528109	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs536841	1.00[YRI][hapmap]
rs542167	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs544458	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs547767	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs548121	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs585820	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs588076	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs592297	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs592314	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs595972	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs596864	0.98[ASN][1000 genomes]
rs600258	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs600743	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs601185	0.81[CHB][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs603615	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs606505	0.82[AFR][1000 genomes]
rs616555	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs618629	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs618679	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs622220	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs626542	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs627818	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs634719	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs635168	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs637304	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs639012	0.82[AFR][1000 genomes]
rs648270	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs654194	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs655641	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs659801	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs669556	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs669813	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs670606	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs673751	0.83[AFR][1000 genomes]
rs677909	1.00[YRI][hapmap]
rs682366	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs682928	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs683340	0.93[ASN][1000 genomes]
rs75751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7951988	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs867611	1.00[YRI][hapmap]
rs9804630	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1048818	chr11:85524635-85746473	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv541116	chr11:85524635-85746473	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1053808	chr11:85588919-85757693	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1053599	chr11:85641619-85684353	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1040567	chr11:85641619-85684935	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85646600-85667400	Weak transcription	Gastric	stomach
2	chr11:85652800-85668800	Weak transcription	Small Intestine	intestine
3	chr11:85656000-85679800	Weak transcription	Fetal Brain Male	brain
4	chr11:85657600-85666600	Weak transcription	Spleen	Spleen
5	chr11:85658400-85666600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:85658400-85667400	Weak transcription	Pancreas	Pancrea
7	chr11:85658600-85667400	Weak transcription	Esophagus	oesophagus
8	chr11:85658600-85673000	Weak transcription	Right Ventricle	heart
9	chr11:85659400-85745800	Weak transcription	Stomach Mucosa	stomach
10	chr11:85659800-85666800	Weak transcription	Fetal Lung	lung
11	chr11:85660200-85666600	Weak transcription	HUVEC	blood vessel
12	chr11:85660200-85670800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:85660400-85666600	Weak transcription	NHEK	skin
14	chr11:85660400-85667400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:85663400-85692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:85663600-85666800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:85663800-85740200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr11:85664200-85666800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:85664200-85668200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:85664200-85673000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:85664400-85667200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:85664400-85667600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:85664400-85667600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:85664400-85667800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:85664400-85667800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:85664400-85668000	Enhancers	Ovary	ovary
27	chr11:85664400-85668200	Strong transcription	Fetal Intestine Large	intestine
28	chr11:85664400-85673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:85664400-85678600	Strong transcription	Adipose Nuclei	Adipose
30	chr11:85664400-85687200	Strong transcription	Primary T cells from cord blood	blood
31	chr11:85664400-85693600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:85664400-85699800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:85664400-85726800	Strong transcription	Liver	Liver
34	chr11:85664400-85729000	Strong transcription	Placenta	Placenta
35	chr11:85664600-85667800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr11:85664600-85668000	Strong transcription	Fetal Stomach	stomach
37	chr11:85664600-85668000	Strong transcription	Thymus	Thymus
38	chr11:85664600-85673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:85664600-85693200	Strong transcription	Fetal Thymus	thymus
40	chr11:85664600-85730800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:85664800-85666800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr11:85664800-85674200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:85664800-85678600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr11:85664800-85689400	Strong transcription	Primary B cells from cord blood	blood
45	chr11:85664800-85733000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr11:85665000-85666600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:85665000-85666600	Weak transcription	Brain Germinal Matrix	brain
48	chr11:85665000-85667600	Genic enhancers	Osteobl	bone
49	chr11:85665000-85668000	Genic enhancers	Fetal Muscle Leg	muscle
50	chr11:85665000-85671000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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