Variant report

Variant	rs1379111
Chromosome Location	chr5:59994098-59994099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:59933171..59934818-chr5:59991480..59994360,2	K562	blood:
2	chr5:59994096..59995835-chr5:60107793..60109955,2	MCF-7	breast:
3	chr5:59993591..59996148-chr5:60625919..60628980,4	K562	blood:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1026418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107232	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs1107233	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs12658660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379113	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460959	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs1563516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[ASN][1000 genomes]
rs1563517	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs1563518	0.91[CHB][hapmap]
rs1563519	0.93[CHB][hapmap]
rs1563905	0.93[CHB][hapmap]
rs1563906	0.91[CHB][hapmap]
rs1563907	0.93[CHB][hapmap]
rs16878304	1.00[CEU][hapmap]
rs16878315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878354	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1870012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1870013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992613	0.93[CHB][hapmap]
rs2045355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap]
rs2124751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124753	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2169254	0.93[CHB][hapmap]
rs2305680	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs2591635	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.94[YRI][hapmap]
rs2606688	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs286150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap]
rs286152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap]
rs286157	1.00[CEU][hapmap]
rs2898298	0.93[CHB][hapmap]
rs34414908	0.83[ASN][1000 genomes]
rs34915115	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857238	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs4273559	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs61752571	0.85[ASN][1000 genomes]
rs6871928	0.93[CHB][hapmap]
rs6872509	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7702459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7708849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7713673	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7716051	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs7719525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733069	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs881066	0.82[ASN][1000 genomes]
rs897671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897673	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv1816307	chr5:59992305-60012235	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59969600-59994800	Weak transcription	Fetal Lung	lung
2	chr5:59971000-59994200	Weak transcription	NH-A	brain
3	chr5:59974200-59994200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:59977200-59994800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:59980200-59995200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:59981800-59994200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:59982600-59994800	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:59982800-59994800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:59982800-59994800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:59983000-59994200	Weak transcription	Thymus	Thymus
11	chr5:59983000-59994600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:59983000-59994800	Weak transcription	Fetal Thymus	thymus
13	chr5:59983000-59994800	Weak transcription	HSMM	muscle
14	chr5:59984600-59994800	Weak transcription	Fetal Intestine Small	intestine
15	chr5:59991400-59994200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:59991400-59994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:59991400-59994800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:59991400-59994800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:59991400-59995000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:59991400-59995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:59991400-59995200	Weak transcription	Pancreas	Pancrea
22	chr5:59991600-59994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:59991600-59994400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:59991600-59994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:59991800-59995200	Weak transcription	Psoas Muscle	Psoas
26	chr5:59992400-59994200	Enhancers	HepG2	liver
27	chr5:59992400-59994800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:59992600-59994800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:59992600-59996600	Active TSS	GM12878-XiMat	blood
30	chr5:59993000-59994200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr5:59993000-59994600	Enhancers	NHDF-Ad	bronchial
32	chr5:59993000-59994800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:59993000-59994800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr5:59993000-59996400	Active TSS	Placenta	Placenta
35	chr5:59993200-59994200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:59993200-59994600	Enhancers	HMEC	breast
37	chr5:59993200-59994800	Enhancers	HUVEC	blood vessel
38	chr5:59993400-59994200	Weak transcription	Fetal Brain Male	brain
39	chr5:59993400-59994200	Weak transcription	Fetal Intestine Large	intestine
40	chr5:59993400-59994200	Weak transcription	NHEK	skin
41	chr5:59993400-59994800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:59993400-59994800	Enhancers	A549	lung
43	chr5:59993600-59994600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:59993800-59994600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:59993800-59994600	Enhancers	NHLF	lung
46	chr5:59994000-59994200	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr5:59994000-59994200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:59994000-59994200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr5:59994000-59994400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:59994000-59994400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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