Variant report

Variant	rs10506293
Chromosome Location	chr12:50796319-50796320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50795879..50797710-chr12:50805639..50808628,2	MCF-7	breast:
2	chr12:50795980..50797892-chr12:50802971..50805412,2	MCF-7	breast:
3	chr12:50787607..50792856-chr12:50793045..50797935,10	K562	blood:

Variant related genes	Relation type
ENSG00000185958	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10747580	0.92[ASN][1000 genomes]
rs10747581	0.92[ASN][1000 genomes]
rs10783348	0.85[MEX][hapmap]
rs10783362	0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10783368	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10876030	0.86[ASN][1000 genomes]
rs10876034	0.85[ASN][1000 genomes]
rs10876048	0.85[EUR][1000 genomes]
rs10876054	0.85[EUR][1000 genomes]
rs11169408	0.87[ASN][1000 genomes]
rs11169422	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169427	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11169440	0.85[ASN][1000 genomes]
rs11503904	0.81[ASN][1000 genomes]
rs12099511	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12099615	0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs12296379	0.90[EUR][1000 genomes]
rs12307602	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12320201	0.85[EUR][1000 genomes]
rs12578525	0.86[ASN][1000 genomes]
rs13328926	0.90[EUR][1000 genomes]
rs1402693	0.90[EUR][1000 genomes]
rs17119774	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[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];0.99[ASN][1000 genomes]
rs17119778	0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs17124672	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17531020	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1996750	0.90[EUR][1000 genomes]
rs2684902	0.85[EUR][1000 genomes]
rs28414775	0.90[EUR][1000 genomes]
rs28479152	0.90[EUR][1000 genomes]
rs2947617	0.85[EUR][1000 genomes]
rs4129355	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4238104	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4257057	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4298982	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4306347	0.90[EUR][1000 genomes]
rs4351895	0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4450234	0.89[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4517607	0.90[EUR][1000 genomes]
rs4562889	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4768877	0.91[ASN][1000 genomes]
rs4768878	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4768879	0.86[ASN][1000 genomes]
rs4768880	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4768887	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4768928	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4768936	0.94[ASN][1000 genomes]
rs56150799	0.81[AMR][1000 genomes]
rs56671180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56753963	0.90[EUR][1000 genomes]
rs56989201	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57283487	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57293958	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57512759	0.90[EUR][1000 genomes]
rs57578212	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57811009	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57828015	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58500867	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58869591	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58888905	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58915267	0.94[EUR][1000 genomes]
rs58916974	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59163743	0.85[AMR][1000 genomes]
rs59194948	0.90[EUR][1000 genomes]
rs59683461	0.90[EUR][1000 genomes]
rs59696942	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59968707	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60010359	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60198651	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60201334	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60239257	0.90[EUR][1000 genomes]
rs60242613	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60396677	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60420087	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60494920	0.90[EUR][1000 genomes]
rs60610745	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60743903	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61578731	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580745	0.81[AMR][1000 genomes]
rs6580753	0.86[ASN][1000 genomes]
rs6580754	0.86[ASN][1000 genomes]
rs7131993	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7133488	0.95[ASN][1000 genomes]
rs7135159	0.90[ASN][1000 genomes]
rs7135222	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7138063	0.85[ASN][1000 genomes]
rs7295610	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7296212	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7299321	0.95[ASN][1000 genomes]
rs7301125	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7302749	0.85[EUR][1000 genomes]
rs7304017	0.85[ASN][1000 genomes]
rs7304262	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7306387	0.90[EUR][1000 genomes]
rs74090120	0.86[AMR][1000 genomes]
rs7487645	0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7953880	0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7955176	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7955310	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7957033	0.85[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7965165	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7974480	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[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];0.99[ASN][1000 genomes]
rs7978443	0.90[EUR][1000 genomes]
rs7978625	0.80[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7979184	0.84[EUR][1000 genomes]
rs9634264	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv469376	chr12:50792846-50856613	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
9	nsv558841	chr12:50792846-50856613	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv470291	chr12:50792846-50858820	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 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	chr12:50793600-50796800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:50793800-50796400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:50793800-50796400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:50793800-50796400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:50793800-50796600	Active TSS	Hela-S3	cervix
6	chr12:50793800-50797000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:50793800-50797000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:50793800-50797000	Active TSS	Fetal Intestine Large	intestine
9	chr12:50793800-50797400	Active TSS	K562	blood
10	chr12:50793800-50798000	Active TSS	GM12878-XiMat	blood
11	chr12:50794000-50796400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:50794000-50796400	Active TSS	Brain Angular Gyrus	brain
13	chr12:50794000-50796400	Active TSS	Brain Cingulate Gyrus	brain
14	chr12:50794000-50796400	Active TSS	Fetal Muscle Leg	muscle
15	chr12:50794000-50796400	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr12:50794000-50796400	Active TSS	Stomach Mucosa	stomach
17	chr12:50794000-50796400	Active TSS	NH-A	brain
18	chr12:50794000-50796600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:50794000-50796600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:50794000-50796600	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr12:50794000-50796600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:50794000-50796600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:50794000-50796600	Active TSS	Colonic Mucosa	Colon
24	chr12:50794000-50796600	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr12:50794000-50796800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr12:50794000-50796800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr12:50794000-50796800	Active TSS	Aorta	Aorta
28	chr12:50794000-50796800	Active TSS	Fetal Intestine Small	intestine
29	chr12:50794000-50796800	Active TSS	A549	lung
30	chr12:50794000-50796800	Active TSS	HSMMtube	muscle
31	chr12:50794000-50797000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr12:50794000-50797200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:50794000-50797400	Active TSS	NHLF	lung
34	chr12:50794000-50797600	Active TSS	Right Ventricle	heart
35	chr12:50794000-50797800	Active TSS	Psoas Muscle	Psoas
36	chr12:50794000-50798200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:50794200-50796400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr12:50794200-50796400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:50794200-50796400	Active TSS	Brain Anterior Caudate	brain
40	chr12:50794200-50796400	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr12:50794200-50796400	Active TSS	NHDF-Ad	bronchial
42	chr12:50794200-50796600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:50794200-50796600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:50794200-50796600	Active TSS	Muscle Satellite Cultured Cells	--
45	chr12:50794200-50796600	Active TSS	Left Ventricle	heart
46	chr12:50794200-50796800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:50794200-50796800	Active TSS	Fetal Kidney	kidney
48	chr12:50794200-50796800	Active TSS	HSMM	muscle
49	chr12:50794200-50797000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:50794200-50797000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links