Variant report

Variant	rs727376
Chromosome Location	chr2:40000487-40000488
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:39999680-40000508	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39997806..40003955-chr2:40003961..40007756,6	MCF-7	breast:
2	chr2:39909390..39911752-chr2:39999764..40002592,2	K562	blood:
3	chr2:39981401..39983374-chr2:39998682..40001306,2	K562	blood:
4	chr2:40000146..40001663-chr3:101262826..101264500,2	MCF-7	breast:

Variant related genes	Relation type
THUMPD2	TF binding region
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10164984	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10169390	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10174709	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206408	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10207589	0.83[EUR][1000 genomes]
rs10211306	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035138	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035139	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124691	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124692	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11124693	0.87[EUR][1000 genomes]
rs12470473	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12617624	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12620957	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12623462	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12623545	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12624217	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712653	0.84[ASN][1000 genomes]
rs12712656	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13026313	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13400213	0.91[EUR][1000 genomes]
rs13425906	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13428837	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1548877	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17478972	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1986876	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041735	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2058620	0.81[ASN][1000 genomes]
rs2110656	0.83[ASN][1000 genomes]
rs2192685	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2373689	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2540226	0.81[ASN][1000 genomes]
rs2540227	0.82[ASN][1000 genomes]
rs2716730	0.80[EUR][1000 genomes]
rs35761077	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732121	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732122	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670955	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670956	0.83[ASN][1000 genomes]
rs4670957	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670958	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670959	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59756273	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544242	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6719179	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6731026	0.85[ASN][1000 genomes]
rs6731450	0.86[ASN][1000 genomes]
rs6747842	0.86[ASN][1000 genomes]
rs6750252	0.86[ASN][1000 genomes]
rs6758453	0.86[ASN][1000 genomes]
rs7560642	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7581406	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7590912	0.80[EUR][1000 genomes]
rs7591347	0.80[EUR][1000 genomes]
rs8265	0.81[EUR][1000 genomes]
rs917960	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917963	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9309042	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs962262	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs997976	0.84[EUR][1000 genomes];0.91[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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
4	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
6	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain
8	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:39985800-40005400	Weak transcription	Lung	lung
11	chr2:39986000-40004200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:39986200-40004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:39987400-40001000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:39987400-40001000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:39987600-40001000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:39987600-40003200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:39988000-40004400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:39992000-40004400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:39992000-40004600	Weak transcription	Fetal Kidney	kidney
20	chr2:39996400-40001000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:39996400-40004200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:39996400-40005000	Weak transcription	Stomach Mucosa	stomach
23	chr2:39996600-40004600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:39997000-40001000	Weak transcription	Pancreas	Pancrea
25	chr2:39997000-40003400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:39997000-40003400	Weak transcription	Fetal Intestine Large	intestine
27	chr2:39997000-40004200	Weak transcription	Thymus	Thymus
28	chr2:39997000-40004400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:39997000-40004400	Weak transcription	Fetal Stomach	stomach
30	chr2:39997000-40004400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:39997000-40004800	Weak transcription	Fetal Intestine Small	intestine
32	chr2:39997000-40005200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:39997000-40005400	Weak transcription	Placenta	Placenta
34	chr2:39997000-40005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:39997200-40004200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:39997600-40003800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:39998200-40001000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr2:39998600-40004400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:39998600-40004400	Weak transcription	Liver	Liver
40	chr2:39998800-40004000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr2:39999000-40001000	Weak transcription	HepG2	liver
42	chr2:39999000-40004400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:39999000-40005400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:39999200-40001000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:39999200-40001200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:39999200-40002000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:39999400-40001000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:39999400-40001400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:39999400-40002600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:39999600-40000600	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links