Variant report

Variant	rs12475871
Chromosome Location	chr2:153516831-153516832
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	POLR2A	chr2:153516664-153517233	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:153516738-153518383	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:153509462..153511338-chr2:153515994..153518973,2	K562	blood:
2	chr2:153516162..153518944-chr2:153526329..153528091,2	MCF-7	breast:
3	chr2:153516775..153519458-chr2:153520976..153522617,2	K562	blood:

Variant related genes	Relation type
PRPF40A	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10497113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10931263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10931271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10931279	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1135617	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11674911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11676069	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11694512	1.00[ASN][1000 genomes]
rs11901227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12478681	1.00[ASN][1000 genomes]
rs12693429	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12989903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12990935	1.00[CHB][hapmap]
rs12995388	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003670	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13006652	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13014141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13017131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13022436	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13023779	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023975	0.84[EUR][1000 genomes]
rs1370499	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831440	0.84[EUR][1000 genomes]
rs16831456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17328776	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400456	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400952	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2083097	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346551	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34199006	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34454505	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34469468	0.84[EUR][1000 genomes]
rs34619076	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34775858	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35002744	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35421285	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35754252	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35894330	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35937874	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36107565	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36122595	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811569	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4575677	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6434172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66492085	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66849546	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6736003	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71417232	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71417235	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72871148	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591590	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7598878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[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	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153472000-153522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:153495400-153517400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:153497000-153531800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:153497200-153521200	Weak transcription	Esophagus	oesophagus
5	chr2:153500400-153517200	Weak transcription	Hela-S3	cervix
6	chr2:153501400-153531800	Weak transcription	Aorta	Aorta
7	chr2:153504400-153538200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:153505000-153517400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:153505000-153517400	Weak transcription	Gastric	stomach
10	chr2:153505000-153517400	Weak transcription	Right Ventricle	heart
11	chr2:153505000-153540200	Strong transcription	Fetal Thymus	thymus
12	chr2:153505400-153517000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:153505400-153539200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:153505400-153540200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:153505600-153534400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:153505600-153537000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:153505600-153538400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:153506000-153538000	Strong transcription	Liver	Liver
19	chr2:153506200-153539800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:153506200-153546800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:153507000-153523000	Strong transcription	HUVEC	blood vessel
22	chr2:153507000-153538400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:153507000-153541600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:153507200-153538200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:153507400-153530200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:153507600-153526800	Weak transcription	Stomach Mucosa	stomach
27	chr2:153508000-153542000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:153508000-153550800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:153508200-153532800	Strong transcription	HSMM	muscle
30	chr2:153508200-153533600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:153508400-153517800	Strong transcription	HepG2	liver
32	chr2:153508400-153537600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr2:153508400-153537800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:153508400-153538000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:153508400-153538200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:153508400-153538400	Strong transcription	A549	lung
37	chr2:153508600-153529200	Strong transcription	Primary T cells from cord blood	blood
38	chr2:153508600-153539600	Strong transcription	Dnd41	blood
39	chr2:153508800-153535000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:153508800-153540400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr2:153509000-153539600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:153509200-153520800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:153509200-153521400	Strong transcription	Placenta	Placenta
44	chr2:153509200-153551200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:153509400-153538400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:153509800-153535000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:153509800-153540000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:153510000-153530200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr2:153510400-153539400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:153510400-153539600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links