Variant report

Variant	rs6544226
Chromosome Location	chr2:39652485-39652486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39647976..39656890-chr2:39661783..39666548,15	MCF-7	breast:
2	chr2:39652432..39656926-chr2:39657241..39661273,4	MCF-7	breast:
3	chr2:39651403..39653951-chr2:39655387..39658790,4	K562	blood:
4	chr2:39652295..39654468-chr2:39663435..39665113,2	MCF-7	breast:
5	chr2:39652451..39655493-chr2:39655687..39657617,3	K562	blood:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10196253	0.94[ASN][1000 genomes]
rs11124681	1.00[ASN][1000 genomes]
rs11688998	0.94[ASN][1000 genomes]
rs17023504	0.89[ASN][1000 genomes]
rs17023656	0.94[ASN][1000 genomes]
rs17023777	0.94[ASN][1000 genomes]
rs3755175	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3770676	0.89[ASN][1000 genomes]
rs3770677	0.89[ASN][1000 genomes]
rs3770679	0.89[ASN][1000 genomes]
rs55748017	0.89[ASN][1000 genomes]
rs56833014	0.94[ASN][1000 genomes]
rs57103739	0.89[ASN][1000 genomes]
rs57232122	0.94[ASN][1000 genomes]
rs58704884	0.94[ASN][1000 genomes]
rs60192971	0.94[ASN][1000 genomes]
rs61480659	0.94[ASN][1000 genomes]
rs6721049	0.86[AMR][1000 genomes]
rs7591102	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39637200-39659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:39639200-39658000	Weak transcription	Fetal Stomach	stomach
3	chr2:39639600-39657200	Weak transcription	HMEC	breast
4	chr2:39640800-39656800	Weak transcription	NH-A	brain
5	chr2:39640800-39660000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:39641000-39656600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:39641200-39659600	Weak transcription	Brain Angular Gyrus	brain
8	chr2:39644200-39661600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:39644400-39654200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:39644400-39654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:39645000-39658800	Weak transcription	Brain Anterior Caudate	brain
12	chr2:39645200-39658200	Weak transcription	Right Ventricle	heart
13	chr2:39646000-39660200	Weak transcription	Fetal Intestine Small	intestine
14	chr2:39646200-39653200	Weak transcription	Stomach Mucosa	stomach
15	chr2:39646200-39656200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:39646200-39658000	Weak transcription	Liver	Liver
17	chr2:39647000-39657400	Weak transcription	Adipose Nuclei	Adipose
18	chr2:39647200-39652600	Weak transcription	Fetal Heart	heart
19	chr2:39647200-39658400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:39647200-39659000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:39647400-39654200	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:39647400-39656600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:39647400-39657800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:39647400-39658400	Weak transcription	Small Intestine	intestine
25	chr2:39647400-39658600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:39647800-39660200	Weak transcription	Pancreas	Pancrea
27	chr2:39648000-39654200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:39648400-39658200	Weak transcription	Aorta	Aorta
29	chr2:39649600-39654000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:39649800-39659200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:39650000-39658600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:39650200-39653200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr2:39650200-39655200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:39650200-39655200	Enhancers	HepG2	liver
35	chr2:39650400-39653600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr2:39650400-39655400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr2:39650600-39654400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:39650600-39656600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:39650800-39653000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:39651400-39652800	Enhancers	Primary hematopoietic stem cells	blood
41	chr2:39651400-39652800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:39651400-39652800	Enhancers	Fetal Thymus	thymus
43	chr2:39651400-39652800	Enhancers	Left Ventricle	heart
44	chr2:39651400-39653000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:39651400-39653400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:39651400-39653800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:39651400-39655200	Enhancers	Dnd41	blood
48	chr2:39651600-39652600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:39651600-39652800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr2:39651600-39653000	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links