Variant report

Variant	rs10506277
Chromosome Location	chr12:48594619-48594620
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48593487..48595723-chr12:48689162..48691231,3	K562	blood:
2	chr12:48591422..48593721-chr12:48594349..48596928,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1004746	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1004806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506276	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10506278	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs10506280	0.87[AMR][1000 genomes]
rs11830378	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11830864	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11833380	0.89[AMR][1000 genomes]
rs11834109	1.00[CEU][hapmap]
rs11837419	0.89[AMR][1000 genomes]
rs11837548	0.89[AMR][1000 genomes]
rs11837571	0.89[AMR][1000 genomes]
rs17122802	0.87[EUR][1000 genomes]
rs17122906	0.87[AMR][1000 genomes]
rs17122918	1.00[CEU][hapmap]
rs17122920	1.00[CEU][hapmap]
rs17224674	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17224828	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17225198	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs17225261	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225366	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225751	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17226359	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17226506	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17226723	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17823193	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17823313	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823415	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823565	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs17824200	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17824705	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17824989	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17825013	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2228501	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3936179	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4075914	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41291959	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41291961	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55638557	0.89[AMR][1000 genomes]
rs55654871	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55682541	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55707383	0.84[EUR][1000 genomes]
rs55752728	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55763362	0.87[AMR][1000 genomes]
rs55794326	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55854069	0.87[AMR][1000 genomes]
rs55886138	0.81[EUR][1000 genomes]
rs55890195	0.96[EUR][1000 genomes]
rs55894137	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55920439	0.87[AMR][1000 genomes]
rs55945889	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55953382	0.84[EUR][1000 genomes]
rs56049209	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56084718	0.87[AMR][1000 genomes]
rs56110736	0.87[AMR][1000 genomes]
rs56116946	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56187356	0.96[EUR][1000 genomes]
rs56205628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56271815	0.87[AMR][1000 genomes]
rs56288528	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56378908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56383074	0.87[AMR][1000 genomes]
rs56389692	0.87[AMR][1000 genomes]
rs56412095	0.87[AMR][1000 genomes]
rs6580666	0.87[AMR][1000 genomes]
rs7138353	0.89[AMR][1000 genomes]
rs7297558	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs7301153	0.87[CEU][hapmap];0.89[AMR][1000 genomes]
rs7301509	0.87[CEU][hapmap];0.89[AMR][1000 genomes]
rs7307383	0.89[AMR][1000 genomes]
rs7307676	0.89[AMR][1000 genomes]
rs7307874	0.87[CEU][hapmap];0.89[AMR][1000 genomes]
rs7310715	0.89[AMR][1000 genomes]
rs7310935	0.87[CEU][hapmap];0.89[AMR][1000 genomes]
rs73304917	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74089155	0.96[EUR][1000 genomes]
rs74089159	0.85[EUR][1000 genomes]
rs74089163	0.85[EUR][1000 genomes]
rs751315	0.87[AMR][1000 genomes]
rs751316	0.87[AMR][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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10506277	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48592400-48594800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:48592600-48595200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:48592800-48594800	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr12:48592800-48595200	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr12:48592800-48596000	Weak transcription	Gastric	stomach
6	chr12:48592800-48596000	Weak transcription	Ovary	ovary
7	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:48593000-48595000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:48593000-48595600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr12:48593000-48595600	Enhancers	Placenta	Placenta
11	chr12:48593000-48596600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:48593200-48594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:48593200-48595000	Enhancers	Adipose Nuclei	Adipose
14	chr12:48593200-48595000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr12:48593200-48595200	Enhancers	Psoas Muscle	Psoas
16	chr12:48593200-48596800	Weak transcription	Brain Substantia Nigra	brain
17	chr12:48593200-48599000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:48593200-48600200	Weak transcription	Right Ventricle	heart
19	chr12:48593400-48596000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:48593600-48595200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr12:48593600-48596600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:48593800-48594800	Enhancers	Rectal Smooth Muscle	rectum
24	chr12:48593800-48595200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:48593800-48596000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:48593800-48596000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:48593800-48596000	Weak transcription	Fetal Stomach	stomach
28	chr12:48593800-48596400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:48593800-48596600	Weak transcription	Left Ventricle	heart
30	chr12:48593800-48598400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:48593800-48598400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:48594000-48595000	Weak transcription	Small Intestine	intestine
33	chr12:48594000-48595200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:48594000-48595200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:48594000-48595200	Enhancers	Brain Anterior Caudate	brain
36	chr12:48594000-48595200	Enhancers	Fetal Lung	lung
37	chr12:48594000-48595600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:48594000-48595800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:48594000-48596800	Enhancers	Primary T cells fromperipheralblood	blood
40	chr12:48594000-48598400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:48594200-48595000	Weak transcription	K562	blood
42	chr12:48594200-48595200	Enhancers	Primary hematopoietic stem cells	blood
43	chr12:48594200-48595200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr12:48594200-48595200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:48594200-48595200	Enhancers	Thymus	Thymus
46	chr12:48594200-48595800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:48594200-48595800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:48594200-48596400	Weak transcription	Fetal Kidney	kidney
49	chr12:48594200-48598600	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:48594200-48598800	Weak transcription	Fetal Heart	heart

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