Variant report

Variant	rs12784928
Chromosome Location	chr10:1083617-1083618
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:1082912..1084464-chr10:1086801..1088755,2	MCF-7	breast:
2	chr10:1038435..1041115-chr10:1083089..1086536,3	K562	blood:
3	chr10:1083077..1085466-chr10:1096305..1099633,3	MCF-7	breast:
4	chr10:1080311..1084643-chr10:1093225..1095856,7	MCF-7	breast:
5	chr10:1071929..1076596-chr10:1081976..1085253,4	K562	blood:
6	chr10:1002935..1005856-chr10:1082299..1084442,2	MCF-7	breast:
7	chr10:1082960..1085323-chr10:1085566..1087572,2	MCF-7	breast:
8	chr10:1082418..1085956-chr10:1093172..1097957,6	MCF-7	breast:
9	chr10:1082336..1085683-chr10:1088908..1090721,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000238924	Chromatin interaction
ENSG00000067064	Chromatin interaction
ENSG00000047056	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10508206	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11250228	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11814057	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12762955	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12767171	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777800	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12783621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131826	1.00[JPT][hapmap]
rs2127604	1.00[JPT][hapmap]
rs28512382	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34159706	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34884971	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35657988	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41260144	0.82[EUR][1000 genomes]
rs4463782	0.83[ASN][1000 genomes]
rs66797613	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67205460	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67696450	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7072554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7094905	1.00[JPT][hapmap]
rs7100196	1.00[CHB][hapmap];0.86[YRI][hapmap]
rs71491334	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer 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	41 gene(s)	inside rSNPs	diseases
7	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh 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
10	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
17	nsv1040178	chr10:1024910-1126104	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv540410	chr10:1024910-1126104	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv894722	chr10:1058837-1274538	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
20	nsv1046220	chr10:1064024-1188998	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
21	nsv894723	chr10:1073684-1259485	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
22	nsv5532	chr10:1079499-1101700	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12784928	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1035000-1094000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:1060000-1091600	Weak transcription	Hela-S3	cervix
3	chr10:1063200-1092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:1063600-1088200	Weak transcription	Fetal Brain Male	brain
5	chr10:1064000-1084400	Weak transcription	Colonic Mucosa	Colon
6	chr10:1064000-1088400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr10:1065200-1084800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr10:1065600-1083800	Weak transcription	Fetal Lung	lung
9	chr10:1065600-1086000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:1065600-1086200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr10:1065800-1086200	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:1065800-1087800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:1066000-1086000	Weak transcription	HSMMtube	muscle
14	chr10:1066200-1085200	Weak transcription	HUVEC	blood vessel
15	chr10:1066200-1086000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr10:1066200-1086200	Weak transcription	Fetal Kidney	kidney
17	chr10:1066600-1084000	Weak transcription	Placenta	Placenta
18	chr10:1066600-1088200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:1066800-1083800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:1066800-1083800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:1066800-1083800	Weak transcription	NHLF	lung
22	chr10:1066800-1084000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:1066800-1085000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr10:1066800-1085200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr10:1066800-1085600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr10:1066800-1085800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:1067000-1085200	Weak transcription	HSMM	muscle
28	chr10:1067200-1086200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr10:1067400-1089400	Weak transcription	Pancreas	Pancrea
30	chr10:1070800-1085800	Weak transcription	Osteobl	bone
31	chr10:1073400-1091800	Weak transcription	Fetal Heart	heart
32	chr10:1076600-1086800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:1079800-1087800	Weak transcription	Ovary	ovary
34	chr10:1080200-1086200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:1081600-1083800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:1081600-1084000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:1081600-1085000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr10:1081600-1089600	Weak transcription	Psoas Muscle	Psoas
39	chr10:1081800-1084000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr10:1081800-1085200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:1081800-1086200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:1081800-1086200	Weak transcription	HepG2	liver
43	chr10:1081800-1089200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr10:1082000-1089800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr10:1082200-1084000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr10:1082200-1086800	Strong transcription	Primary T cells from cord blood	blood
47	chr10:1082200-1086800	Strong transcription	Fetal Brain Female	brain
48	chr10:1082400-1084000	Strong transcription	Primary B cells from cord blood	blood
49	chr10:1082400-1084000	Genic enhancers	Brain Inferior Temporal Lobe	brain
50	chr10:1082400-1084000	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links