Variant report

Variant	rs11753390
Chromosome Location	chr6:37988189-37988190
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37786879..37788861-chr6:37985416..37988251,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11544071	0.80[EUR][1000 genomes]
rs11751393	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11752354	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs11753809	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755262	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755592	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11755824	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11757086	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11757371	1.00[CEU][hapmap]
rs11757622	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757695	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11759754	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890376	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17512095	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17641690	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17648097	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17648426	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17648634	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17648699	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649606	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17649630	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2036124	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2842505	1.00[JPT][hapmap]
rs55898002	0.85[ASN][1000 genomes]
rs56100831	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56136126	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59522592	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs59810748	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60672298	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60943435	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60977329	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61125348	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61521259	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61705055	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68148876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910601	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6925259	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930340	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849350	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72849354	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72849359	0.80[EUR][1000 genomes]
rs72849369	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72850806	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850831	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850855	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850856	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850871	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850884	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72850893	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72852516	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852536	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852555	1.00[AFR][1000 genomes]
rs72852565	0.85[ASN][1000 genomes]
rs72852588	0.85[ASN][1000 genomes]
rs7739801	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7747199	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7767466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs994530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv34450	chr6:37963308-38007241	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2763549	chr6:37985025-38014006	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37963000-37995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:37976600-37988400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:37979400-37989000	Weak transcription	Primary T cells from cord blood	blood
4	chr6:37981400-37989000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:37981400-37989000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:37981400-37990400	Weak transcription	Fetal Brain Female	brain
7	chr6:37982600-37989400	Weak transcription	Psoas Muscle	Psoas
8	chr6:37983000-37994600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:37983400-37988400	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:37983400-37994600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:37983600-37988200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:37983800-37988400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:37984200-37988400	Weak transcription	Brain Substantia Nigra	brain
14	chr6:37984200-37989400	Enhancers	Liver	Liver
15	chr6:37985000-37989000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:37985000-37995600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:37985000-38002400	Weak transcription	Primary B cells from cord blood	blood
18	chr6:37985000-38030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:37985200-37988400	Weak transcription	Brain Anterior Caudate	brain
20	chr6:37985200-37989000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:37985200-37991400	Weak transcription	GM12878-XiMat	blood
22	chr6:37985200-37995000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:37985200-37995400	Weak transcription	A549	lung
24	chr6:37985200-37995600	Weak transcription	Brain Angular Gyrus	brain
25	chr6:37985200-38001400	Weak transcription	Small Intestine	intestine
26	chr6:37985400-37989000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:37985400-37992200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:37987000-37993600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:37987400-37988600	Enhancers	Right Ventricle	heart
30	chr6:37987400-37990800	Enhancers	Colon Smooth Muscle	Colon
31	chr6:37987600-37989600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:37987600-37989800	Enhancers	Left Ventricle	heart
33	chr6:37987600-37989800	Enhancers	Rectal Smooth Muscle	rectum
34	chr6:37987800-37988400	Weak transcription	Gastric	stomach
35	chr6:37987800-37988400	Weak transcription	Ovary	ovary
36	chr6:37987800-37988400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:37987800-37990000	Enhancers	Stomach Smooth Muscle	stomach
38	chr6:37987800-37990400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr6:37987800-37990800	Enhancers	Fetal Stomach	stomach
40	chr6:37988000-38001400	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links