Variant report

Variant	rs2842529
Chromosome Location	chr6:37986527-37986528
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	chr6:37786879..37788861-chr6:37985416..37988251,2	MCF-7	breast:
2	chr6:37983748..37986719-chr6:38000048..38002009,3	K562	blood:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10456097	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947713	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1187422	0.80[ASN][1000 genomes]
rs1187423	0.80[ASN][1000 genomes]
rs12190306	0.81[EUR][1000 genomes]
rs12192182	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12194618	0.82[EUR][1000 genomes]
rs12194823	0.86[EUR][1000 genomes]
rs12198907	0.80[ASN][1000 genomes]
rs12200258	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12204352	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12206818	0.80[ASN][1000 genomes]
rs12211248	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12211981	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12212723	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12213151	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12213835	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12214375	0.80[EUR][1000 genomes]
rs13210701	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13214465	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13220131	0.92[EUR][1000 genomes]
rs16890344	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs171831	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1812599	0.81[EUR][1000 genomes]
rs2132597	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259673	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs259684	0.84[EUR][1000 genomes]
rs259686	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs259689	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs259690	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs259691	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs259695	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs259713	0.80[ASN][1000 genomes]
rs259715	0.80[ASN][1000 genomes]
rs2645102	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645107	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2645113	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2645116	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645117	0.90[AFR][1000 genomes]
rs2645120	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645124	0.88[AFR][1000 genomes]
rs2645127	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2645128	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2645131	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2645134	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2645137	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842500	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842517	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2842527	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34871463	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35823566	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56098839	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140804	0.83[EUR][1000 genomes]
rs7747130	0.86[EUR][1000 genomes]
rs941850	0.80[EUR][1000 genomes]
rs9647619	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs966705	0.85[EUR][1000 genomes];0.80[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:45 , 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	chr6:37969200-37987800	Weak transcription	Fetal Kidney	kidney
3	chr6:37976600-37988400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:37976800-37987800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:37978200-37987600	Weak transcription	Pancreas	Pancrea
6	chr6:37979400-37989000	Weak transcription	Primary T cells from cord blood	blood
7	chr6:37980000-37986800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:37980600-37987800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:37981400-37989000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:37981400-37989000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:37981400-37990400	Weak transcription	Fetal Brain Female	brain
12	chr6:37982600-37989400	Weak transcription	Psoas Muscle	Psoas
13	chr6:37983000-37994600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:37983400-37988400	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:37983400-37994600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:37983600-37987600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:37983600-37988200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:37983800-37988400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:37984200-37988400	Weak transcription	Brain Substantia Nigra	brain
20	chr6:37984200-37989400	Enhancers	Liver	Liver
21	chr6:37984800-37987000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:37985000-37989000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:37985000-37995600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:37985000-38002400	Weak transcription	Primary B cells from cord blood	blood
25	chr6:37985000-38030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:37985200-37986600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:37985200-37987400	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:37985200-37987600	Weak transcription	Gastric	stomach
29	chr6:37985200-37987600	Weak transcription	Left Ventricle	heart
30	chr6:37985200-37987600	Weak transcription	Ovary	ovary
31	chr6:37985200-37987600	Weak transcription	Right Atrium	heart
32	chr6:37985200-37987800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:37985200-37988400	Weak transcription	Brain Anterior Caudate	brain
34	chr6:37985200-37989000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:37985200-37991400	Weak transcription	GM12878-XiMat	blood
36	chr6:37985200-37995000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:37985200-37995400	Weak transcription	A549	lung
38	chr6:37985200-37995600	Weak transcription	Brain Angular Gyrus	brain
39	chr6:37985200-38001400	Weak transcription	Small Intestine	intestine
40	chr6:37985400-37986800	Weak transcription	Lung	lung
41	chr6:37985400-37987800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:37985400-37989000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:37985400-37992200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:37986200-37986800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr6:37986200-37987200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links