Variant report

Variant	rs317878
Chromosome Location	chr4:16176635-16176636
allele	A/G
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	chr4:16175177-16176650	K562	blood:	n/a	n/a

Variant related genes	Relation type
TAPT1	TF binding region
ENSG00000249234	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10019399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1046234	0.92[YRI][hapmap]
rs10516298	0.87[CHD][hapmap]
rs10516299	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs10939651	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939652	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939653	0.81[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs12506249	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12646600	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13133263	0.90[YRI][hapmap]
rs13634	0.90[YRI][hapmap]
rs1373112	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1619904	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662650	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662654	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662656	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16893158	0.88[CHD][hapmap]
rs16893162	0.90[YRI][hapmap]
rs1712492	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs178450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203434	0.85[YRI][hapmap]
rs2044195	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28453363	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28618674	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28645901	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs317854	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs317855	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs317869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs317870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs317871	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs317872	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs317873	0.90[YRI][hapmap]
rs317874	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs317875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs317876	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs317877	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4395495	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6812660	0.90[YRI][hapmap]
rs894639	0.92[CHD][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs961449	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16157800-16180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:16157800-16180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:16160400-16182400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:16160800-16176800	Strong transcription	Primary B cells from cord blood	blood
5	chr4:16161000-16182600	Strong transcription	Fetal Thymus	thymus
6	chr4:16161600-16181800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:16161600-16182600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:16161600-16182800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:16161600-16186000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:16161800-16193200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr4:16162200-16182800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr4:16162600-16183200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr4:16163000-16182800	Strong transcription	Liver	Liver
14	chr4:16163000-16183200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:16163000-16183200	Strong transcription	Placenta	Placenta
16	chr4:16163200-16178200	Weak transcription	Fetal Heart	heart
17	chr4:16163200-16183400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:16163200-16183400	Weak transcription	Hela-S3	cervix
19	chr4:16163200-16195800	Weak transcription	HMEC	breast
20	chr4:16163800-16178800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:16164000-16181800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:16164200-16183000	Strong transcription	Primary hematopoietic stem cells	blood
23	chr4:16164400-16176800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:16164400-16181000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr4:16164400-16195000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:16164800-16183000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:16165000-16190800	Weak transcription	HUVEC	blood vessel
28	chr4:16167600-16180200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:16168200-16187400	Weak transcription	Osteobl	bone
32	chr4:16168200-16198000	Weak transcription	A549	lung
33	chr4:16168400-16180200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:16168400-16180200	Weak transcription	Brain Angular Gyrus	brain
35	chr4:16168400-16180600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:16168400-16194600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:16168400-16197800	Weak transcription	NHLF	lung
38	chr4:16168400-16198000	Weak transcription	NH-A	brain
39	chr4:16168600-16177800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:16168600-16180200	Weak transcription	Fetal Brain Male	brain
41	chr4:16168600-16180400	Weak transcription	Psoas Muscle	Psoas
42	chr4:16168600-16191000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:16168600-16198000	Weak transcription	NHEK	skin
44	chr4:16169400-16180200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:16170000-16178200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:16170400-16191400	Weak transcription	Colonic Mucosa	Colon
47	chr4:16170600-16191000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:16170800-16180600	Weak transcription	Brain Hippocampus Middle	brain
49	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:16171400-16178200	Weak transcription	Gastric	stomach

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