Variant report

Variant	rs4953470
Chromosome Location	chr2:47379474-47379475
allele	C/T
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	TEAD4	chr2:47379372-47379776	ECC-1	luminal epithelium:	n/a	n/a
2	YY1	chr2:47379401-47379527	K562	blood:	n/a	chr2:47379516-47379524

Variant related genes	Relation type
C2orf61	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11842	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13397696	1.00[CHB][hapmap]
rs13413278	1.00[CHB][hapmap]
rs17036300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036311	0.91[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17036313	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17036316	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17036320	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs17036325	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes]
rs2016682	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2347617	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4953469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953472	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56875665	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59415749	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6544960	1.00[CHB][hapmap]
rs6713257	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6749284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72810414	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72810415	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72810417	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72810419	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72877054	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7583684	0.85[AMR][1000 genomes];0.83[EUR][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47357000-47385400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:47357000-47386600	Weak transcription	Fetal Heart	heart
3	chr2:47357000-47386800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:47357200-47386400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:47357400-47385400	Weak transcription	Fetal Intestine Large	intestine
6	chr2:47360600-47386800	Weak transcription	Stomach Mucosa	stomach
7	chr2:47363400-47386400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:47365000-47384000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:47366000-47383000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:47366200-47397000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:47366600-47380000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:47366800-47399400	Strong transcription	Fetal Thymus	thymus
13	chr2:47367000-47379600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:47367000-47401200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:47367200-47379800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:47367200-47381600	Strong transcription	NHDF-Ad	bronchial
17	chr2:47367200-47382200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:47367200-47383600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:47367200-47402000	Weak transcription	Esophagus	oesophagus
20	chr2:47367600-47382200	Weak transcription	Spleen	Spleen
21	chr2:47367600-47385400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:47367600-47386800	Weak transcription	Right Ventricle	heart
23	chr2:47367600-47387400	Weak transcription	Pancreas	Pancrea
24	chr2:47368800-47385200	Weak transcription	Fetal Intestine Small	intestine
25	chr2:47369000-47385600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:47369200-47386800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:47369600-47384600	Weak transcription	HUVEC	blood vessel
28	chr2:47369600-47386200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:47369800-47386800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:47369800-47386800	Weak transcription	Psoas Muscle	Psoas
31	chr2:47369800-47391200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:47370000-47380800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:47370000-47389600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr2:47370400-47379800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr2:47371000-47381000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:47371200-47385800	Weak transcription	Fetal Kidney	kidney
37	chr2:47371200-47388200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:47371400-47386600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:47371600-47389800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:47371800-47392200	Strong transcription	Osteobl	bone
41	chr2:47372000-47386800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:47372600-47385000	Weak transcription	Fetal Lung	lung
43	chr2:47372600-47386800	Weak transcription	Gastric	stomach
44	chr2:47372600-47396800	Weak transcription	Small Intestine	intestine
45	chr2:47373600-47385400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:47374000-47381000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:47374400-47379800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:47374800-47379800	Strong transcription	NHEK	skin
49	chr2:47374800-47385600	Weak transcription	HepG2	liver
50	chr2:47375400-47386000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links