Variant report

Variant	rs6115248
Chromosome Location	chr20:25653105-25653106
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25604523..25606261-chr20:25653014..25654610,2	MCF-7	breast:
2	chr20:25652247..25655467-chr20:25656048..25658706,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10470065	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11905437	1.00[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap]
rs16987806	1.00[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap]
rs17244452	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2185914	0.91[ASW][hapmap]
rs55652038	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56184302	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6050941	1.00[CHD][hapmap]
rs6107071	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6115193	1.00[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap]
rs6115202	0.84[ASW][hapmap];0.86[YRI][hapmap]
rs6115208	1.00[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6115211	0.88[AFR][1000 genomes]
rs6115223	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6115227	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs6115256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6115349	0.91[ASW][hapmap]
rs6115355	1.00[CHD][hapmap]
rs7272126	1.00[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap]
rs73102106	0.87[EUR][1000 genomes]
rs73102113	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73102121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73111222	0.93[EUR][1000 genomes]
rs73111242	0.82[AFR][1000 genomes]
rs73113144	0.94[AFR][1000 genomes]
rs7363150	0.91[ASW][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25605600-25654600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:25609200-25653400	Weak transcription	Brain Substantia Nigra	brain
3	chr20:25611400-25653200	Weak transcription	Fetal Intestine Small	intestine
4	chr20:25616000-25653600	Weak transcription	Adipose Nuclei	Adipose
5	chr20:25617600-25653400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:25618400-25653600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr20:25618400-25653600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr20:25623200-25653600	Weak transcription	Pancreas	Pancrea
9	chr20:25625000-25655200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr20:25626400-25653600	Weak transcription	Fetal Muscle Leg	muscle
11	chr20:25626800-25654000	Weak transcription	Gastric	stomach
12	chr20:25628200-25653600	Weak transcription	Esophagus	oesophagus
13	chr20:25628800-25653400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr20:25628800-25653400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr20:25628800-25653400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr20:25629000-25653400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr20:25629000-25653600	Weak transcription	Brain Hippocampus Middle	brain
18	chr20:25629000-25653600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr20:25629000-25653800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr20:25632600-25653600	Weak transcription	Brain Anterior Caudate	brain
21	chr20:25641200-25653800	Weak transcription	Right Ventricle	heart
22	chr20:25641600-25653800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr20:25642600-25653400	Weak transcription	Dnd41	blood
24	chr20:25643400-25653400	Weak transcription	A549	lung
25	chr20:25648000-25653600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr20:25648000-25653800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr20:25648600-25653400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr20:25649200-25653200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr20:25649200-25655200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr20:25649400-25653600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr20:25649400-25653800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr20:25649400-25653800	Weak transcription	Spleen	Spleen
33	chr20:25649400-25654400	Weak transcription	Fetal Kidney	kidney
34	chr20:25649600-25653600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr20:25649600-25653600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr20:25649600-25654000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:25649800-25653400	Weak transcription	Thymus	Thymus
38	chr20:25650400-25653600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr20:25650400-25653800	Weak transcription	Primary B cells from cord blood	blood
40	chr20:25650400-25653800	Weak transcription	K562	blood
41	chr20:25650600-25653400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr20:25650600-25655000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr20:25650600-25655800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr20:25650600-25657000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr20:25650800-25653200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr20:25650800-25653400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr20:25650800-25653400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr20:25650800-25653600	Weak transcription	Colon Smooth Muscle	Colon
49	chr20:25650800-25653600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr20:25651000-25653400	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links