Variant report

Variant	rs7112228
Chromosome Location	chr11:100642577-100642578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100556918..100559342-chr11:100641280..100643769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248027	Chromatin interaction
ENSG00000165895	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17095405	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17095409	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17095426	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17095428	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17095429	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17095438	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17095439	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088953	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2407750	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3901516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4087602	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4121392	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4337001	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4469852	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4517481	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs499241	0.89[ASN][1000 genomes]
rs507695	0.81[AMR][1000 genomes]
rs58727919	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60708905	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61890760	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61890763	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61890764	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61890765	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61890766	0.89[ASN][1000 genomes]
rs61892334	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61892352	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61892355	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61910508	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7102634	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105842	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7110872	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7112366	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7116153	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7117515	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7120712	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7126324	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7130855	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73005729	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7927197	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7942588	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7944598	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7947761	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][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	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100624600-100655600	Weak transcription	Left Ventricle	heart
2	chr11:100624600-100655600	Weak transcription	Right Ventricle	heart
3	chr11:100628200-100642800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:100629200-100642800	Weak transcription	Liver	Liver
5	chr11:100631800-100645000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:100632200-100645200	Weak transcription	Colonic Mucosa	Colon
7	chr11:100632200-100647200	Weak transcription	HSMM	muscle
8	chr11:100632800-100645000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:100632800-100645000	Weak transcription	Gastric	stomach
10	chr11:100633000-100647000	Weak transcription	NHLF	lung
11	chr11:100633200-100642600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:100633200-100655600	Weak transcription	Psoas Muscle	Psoas
13	chr11:100633600-100647400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:100635200-100647400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:100635400-100649400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:100635800-100645600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:100636600-100643000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:100637000-100644400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:100639800-100643800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr11:100639800-100645600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:100639800-100647400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:100640000-100648600	Weak transcription	Small Intestine	intestine
23	chr11:100640000-100649600	Weak transcription	Fetal Kidney	kidney
24	chr11:100640000-100655600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr11:100640200-100642800	Weak transcription	Fetal Intestine Small	intestine
26	chr11:100640200-100644200	Weak transcription	Fetal Heart	heart
27	chr11:100640200-100644400	Weak transcription	Fetal Lung	lung
28	chr11:100640200-100644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:100640200-100645000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr11:100640200-100645000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:100640200-100645000	Weak transcription	Fetal Stomach	stomach
32	chr11:100640200-100647000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:100640200-100647200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:100640200-100648600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr11:100640200-100651000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:100640400-100642800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:100640400-100642800	Weak transcription	HSMMtube	muscle
38	chr11:100640400-100645200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr11:100640400-100646600	Weak transcription	Dnd41	blood
40	chr11:100640400-100647000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:100640400-100648800	Weak transcription	Osteobl	bone
42	chr11:100640400-100651000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:100640600-100642800	Weak transcription	Fetal Intestine Large	intestine
44	chr11:100640800-100642600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:100640800-100642600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:100640800-100642800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:100640800-100643000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:100640800-100644000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:100640800-100645400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:100640800-100645800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links