Variant report

Variant	rs6544227
Chromosome Location	chr2:39667634-39667635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39666476..39669114-chr2:39673200..39674751,2	K562	blood:
2	chr2:39539961..39541586-chr2:39667193..39669640,2	K562	blood:
3	chr2:39608115..39611189-chr2:39665899..39668671,3	K562	blood:
4	chr2:39608927..39611189-chr2:39667171..39668738,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10199459	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124683	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11896389	0.89[EUR][1000 genomes]
rs12328714	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17023530	0.91[EUR][1000 genomes]
rs17023542	0.86[EUR][1000 genomes]
rs17023547	0.91[EUR][1000 genomes]
rs17023600	0.91[EUR][1000 genomes]
rs17023611	0.91[EUR][1000 genomes]
rs17023684	0.97[EUR][1000 genomes]
rs17023696	0.97[EUR][1000 genomes]
rs17023773	0.94[EUR][1000 genomes]
rs17446102	0.91[EUR][1000 genomes]
rs17446515	0.91[EUR][1000 genomes]
rs17446690	0.91[EUR][1000 genomes]
rs17505580	0.91[EUR][1000 genomes]
rs17505877	0.91[EUR][1000 genomes]
rs2056653	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2056655	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2111383	0.97[EUR][1000 genomes]
rs2373532	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3732052	0.97[EUR][1000 genomes]
rs4670273	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4670938	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55761128	0.97[EUR][1000 genomes]
rs6544229	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6720537	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6720951	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721740	0.94[EUR][1000 genomes]
rs6731310	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6758596	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73924009	0.97[EUR][1000 genomes]
rs7559436	0.97[EUR][1000 genomes]
rs7577097	0.97[EUR][1000 genomes]
rs7605939	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39665400-39667800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:39665400-39667800	Weak transcription	Esophagus	oesophagus
4	chr2:39665600-39670000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:39665600-39681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:39665600-39684200	Weak transcription	Lung	lung
7	chr2:39665600-39685600	Weak transcription	Left Ventricle	heart
8	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
10	chr2:39665800-39668000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:39665800-39668200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:39665800-39668200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr2:39665800-39668200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:39666000-39681200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:39666200-39681400	Weak transcription	Fetal Intestine Large	intestine
16	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:39666400-39668000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:39666400-39670600	Weak transcription	Liver	Liver
19	chr2:39666600-39667800	Weak transcription	Psoas Muscle	Psoas
20	chr2:39666600-39668200	Enhancers	HepG2	liver
21	chr2:39666600-39671000	Weak transcription	Right Atrium	heart
22	chr2:39666600-39673000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:39666600-39675800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:39666600-39682200	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:39666800-39669400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:39666800-39669600	Weak transcription	Fetal Intestine Small	intestine
27	chr2:39666800-39670800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:39666800-39671400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:39666800-39677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:39666800-39681000	Weak transcription	Brain Substantia Nigra	brain
31	chr2:39666800-39681600	Weak transcription	Ovary	ovary
32	chr2:39667000-39667800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:39667000-39667800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:39667000-39668000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:39667000-39668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:39667000-39668000	Weak transcription	Placenta	Placenta
37	chr2:39667000-39668200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:39667000-39670600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:39667000-39670600	Weak transcription	Aorta	Aorta
40	chr2:39667000-39670800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:39667000-39672400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:39667000-39681400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:39667000-39681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
45	chr2:39667200-39669600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:39667200-39670000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:39667200-39672400	Weak transcription	Fetal Stomach	stomach
48	chr2:39667200-39685200	Weak transcription	NHEK	skin
49	chr2:39667200-39694600	Weak transcription	NHLF	lung
50	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain

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