Variant report

Variant	rs1052420
Chromosome Location	chr10:5920121-5920122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5912116..5916503-chr10:5917203..5921455,4	K562	blood:
2	chr10:5919010..5920872-chr10:5921692..5924189,2	K562	blood:
3	chr10:5918577..5924576-chr10:5927726..5932597,9	MCF-7	breast:
4	chr10:5917302..5921893-chr10:5926757..5932751,9	MCF-7	breast:
5	chr10:5853771..5858349-chr10:5915568..5920799,8	MCF-7	breast:
6	chr10:5913737..5922370-chr10:5922961..5932189,19	K562	blood:

Variant related genes	Relation type
ENSG00000134452	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000272764	Chromatin interaction
ENSG00000057608	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1323659	0.93[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs1707228	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253422	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs2274030	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2669124	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs2669127	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs2761269	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2942348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985042	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]
rs2985043	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]
rs2985044	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584000	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587620	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587655	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593026	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs596156	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs599394	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600706	0.87[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs608197	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609269	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs610335	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622252	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622488	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625073	0.95[ASN][1000 genomes]
rs626040	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627303	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628219	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628234	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628844	0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631538	0.88[ASN][1000 genomes]
rs631947	0.85[EUR][1000 genomes]
rs644474	0.88[CEU][hapmap];0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs646406	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs646490	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.99[ASN][1000 genomes]
rs647391	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs661411	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662701	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]
rs664577	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs664842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665364	0.83[JPT][hapmap]
rs666831	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs672219	0.88[ASN][1000 genomes]
rs672624	0.85[ASN][1000 genomes]
rs673496	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs673678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675416	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs679610	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.99[ASN][1000 genomes]
rs682555	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs684557	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs687191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071536	0.84[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs7075778	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs7091817	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs792342	0.96[ASN][1000 genomes]
rs792347	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs792349	0.96[ASN][1000 genomes]
rs811561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9329328	0.96[ASN][1000 genomes]
rs9424023	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv5654	chr10:5868365-5930634	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5903400-5925000	Weak transcription	Fetal Kidney	kidney
2	chr10:5909600-5924800	Weak transcription	Stomach Mucosa	stomach
3	chr10:5911600-5926800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:5913000-5929800	Weak transcription	Fetal Heart	heart
5	chr10:5913000-5929800	Weak transcription	Psoas Muscle	Psoas
6	chr10:5914000-5929600	Weak transcription	NHLF	lung
7	chr10:5915600-5924400	Weak transcription	Fetal Brain Male	brain
8	chr10:5915600-5930000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr10:5915600-5930000	Weak transcription	HUVEC	blood vessel
10	chr10:5915800-5930000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:5915800-5930200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr10:5916000-5921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr10:5916200-5920400	Strong transcription	Rectal Smooth Muscle	rectum
14	chr10:5916200-5920600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr10:5916200-5921200	Strong transcription	Colon Smooth Muscle	Colon
16	chr10:5916200-5922000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr10:5916200-5922200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:5916200-5922800	Strong transcription	Fetal Stomach	stomach
19	chr10:5916200-5923000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:5916200-5923000	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr10:5916200-5923000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr10:5916200-5925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:5916200-5926400	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr10:5916200-5927600	Strong transcription	Fetal Intestine Small	intestine
25	chr10:5916200-5928200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:5916200-5929000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:5916200-5929400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr10:5916200-5929800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:5916200-5929800	Strong transcription	Fetal Intestine Large	intestine
30	chr10:5916400-5920400	Strong transcription	Ovary	ovary
31	chr10:5916400-5922000	Strong transcription	Fetal Muscle Leg	muscle
32	chr10:5916400-5922200	Strong transcription	Left Ventricle	heart
33	chr10:5916400-5922400	Weak transcription	Primary B cells from cord blood	blood
34	chr10:5916400-5923000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr10:5916400-5924800	Strong transcription	Liver	Liver
36	chr10:5916400-5928200	Strong transcription	Fetal Brain Female	brain
37	chr10:5916400-5929200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr10:5916400-5929800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr10:5916600-5922000	Strong transcription	Gastric	stomach
40	chr10:5916600-5922400	Strong transcription	Brain Substantia Nigra	brain
41	chr10:5916600-5928400	Weak transcription	Small Intestine	intestine
42	chr10:5916600-5929400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:5916600-5930600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr10:5916800-5930200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:5917600-5922600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr10:5917800-5920200	Strong transcription	Placenta	Placenta
47	chr10:5917800-5920600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr10:5917800-5920600	Strong transcription	Pancreas	Pancrea
49	chr10:5917800-5922600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr10:5917800-5927800	Strong transcription	Thymus	Thymus

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