Variant report

Variant	rs34159706
Chromosome Location	chr10:1069190-1069191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:1068741..1070265-chr10:1070445..1072536,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148377	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1013504	1.00[ASN][1000 genomes]
rs10508206	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10903358	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11250228	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11253504	1.00[ASN][1000 genomes]
rs11253518	1.00[ASN][1000 genomes]
rs11253530	1.00[ASN][1000 genomes]
rs11253537	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11253538	1.00[ASN][1000 genomes]
rs11253539	1.00[ASN][1000 genomes]
rs11253540	1.00[ASN][1000 genomes]
rs11253549	1.00[ASN][1000 genomes]
rs11253550	1.00[ASN][1000 genomes]
rs11253557	1.00[ASN][1000 genomes]
rs11253558	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11253559	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11253560	1.00[ASN][1000 genomes]
rs12354710	0.84[AMR][1000 genomes]
rs12354914	1.00[ASN][1000 genomes]
rs12356612	1.00[ASN][1000 genomes]
rs12357633	1.00[ASN][1000 genomes]
rs12359796	1.00[ASN][1000 genomes]
rs1250891	1.00[ASN][1000 genomes]
rs12762955	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12767171	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12768348	1.00[ASN][1000 genomes]
rs12769002	1.00[ASN][1000 genomes]
rs12770173	1.00[ASN][1000 genomes]
rs12771539	1.00[ASN][1000 genomes]
rs12772979	1.00[ASN][1000 genomes]
rs12773961	1.00[ASN][1000 genomes]
rs12774985	1.00[ASN][1000 genomes]
rs12777021	1.00[ASN][1000 genomes]
rs12777800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777801	1.00[ASN][1000 genomes]
rs12778271	1.00[ASN][1000 genomes]
rs12781329	1.00[ASN][1000 genomes]
rs12783621	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12784928	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17221456	1.00[ASN][1000 genomes]
rs17221463	1.00[ASN][1000 genomes]
rs17221491	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17293580	1.00[ASN][1000 genomes]
rs17293608	1.00[ASN][1000 genomes]
rs1871621	1.00[ASN][1000 genomes]
rs1871622	1.00[ASN][1000 genomes]
rs28512382	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34115136	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34270668	1.00[ASN][1000 genomes]
rs34318754	1.00[ASN][1000 genomes]
rs34480046	1.00[ASN][1000 genomes]
rs34487581	1.00[ASN][1000 genomes]
rs34527494	1.00[ASN][1000 genomes]
rs34884971	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34885925	1.00[ASN][1000 genomes]
rs35028518	1.00[ASN][1000 genomes]
rs35306767	1.00[ASN][1000 genomes]
rs35363972	1.00[ASN][1000 genomes]
rs35667562	1.00[ASN][1000 genomes]
rs35670857	1.00[ASN][1000 genomes]
rs35709890	1.00[ASN][1000 genomes]
rs35957139	1.00[ASN][1000 genomes]
rs41260144	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55697724	1.00[ASN][1000 genomes]
rs55708963	1.00[ASN][1000 genomes]
rs55742421	1.00[ASN][1000 genomes]
rs61830926	1.00[ASN][1000 genomes]
rs61830931	1.00[ASN][1000 genomes]
rs61830933	1.00[ASN][1000 genomes]
rs61833260	1.00[ASN][1000 genomes]
rs61833265	1.00[ASN][1000 genomes]
rs66462130	1.00[ASN][1000 genomes]
rs66797613	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67205460	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67696450	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072554	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7075188	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7088956	1.00[ASN][1000 genomes]
rs7093665	1.00[ASN][1000 genomes]
rs7094031	1.00[ASN][1000 genomes]
rs71491334	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72778228	1.00[ASN][1000 genomes]
rs7914758	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv549767	chr10:1064940-1073684	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34159706	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 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	chr10:1049400-1071200	Strong transcription	A549	lung
3	chr10:1049600-1071600	Weak transcription	Fetal Heart	heart
4	chr10:1060000-1091600	Weak transcription	Hela-S3	cervix
5	chr10:1063200-1092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr10:1063600-1088200	Weak transcription	Fetal Brain Male	brain
7	chr10:1064000-1083000	Weak transcription	NHDF-Ad	bronchial
8	chr10:1064000-1084400	Weak transcription	Colonic Mucosa	Colon
9	chr10:1064000-1088400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:1064200-1070000	Weak transcription	Psoas Muscle	Psoas
11	chr10:1064400-1082600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr10:1065200-1084800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr10:1065400-1082800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr10:1065600-1083800	Weak transcription	Fetal Lung	lung
15	chr10:1065600-1086000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:1065600-1086200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:1065800-1082600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr10:1065800-1086200	Weak transcription	Colon Smooth Muscle	Colon
19	chr10:1065800-1087800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:1066000-1070200	Weak transcription	K562	blood
21	chr10:1066000-1080800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:1066000-1081000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr10:1066000-1081200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:1066000-1082000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:1066000-1082400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr10:1066000-1082600	Weak transcription	Aorta	Aorta
27	chr10:1066000-1083000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr10:1066000-1086000	Weak transcription	HSMMtube	muscle
29	chr10:1066200-1069800	Weak transcription	Adipose Nuclei	Adipose
30	chr10:1066200-1070000	Weak transcription	Osteobl	bone
31	chr10:1066200-1079600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:1066200-1082200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr10:1066200-1082200	Weak transcription	NH-A	brain
34	chr10:1066200-1082400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr10:1066200-1083200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr10:1066200-1083400	Weak transcription	Liver	Liver
37	chr10:1066200-1085200	Weak transcription	HUVEC	blood vessel
38	chr10:1066200-1086000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr10:1066200-1086200	Weak transcription	Fetal Kidney	kidney
40	chr10:1066600-1081200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr10:1066600-1082400	Weak transcription	Primary B cells from cord blood	blood
42	chr10:1066600-1082800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr10:1066600-1084000	Weak transcription	Placenta	Placenta
44	chr10:1066600-1088200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr10:1066800-1069600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr10:1066800-1073600	Weak transcription	GM12878-XiMat	blood
47	chr10:1066800-1079600	Weak transcription	Ovary	ovary
48	chr10:1066800-1079600	Weak transcription	HMEC	breast
49	chr10:1066800-1080400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:1066800-1081400	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links