Variant report

Variant	rs17221463
Chromosome Location	chr10:1038040-1038041
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:1032021..1036235-chr10:1037103..1040442,8	MCF-7	breast:
2	chr10:1033990..1039615-chr10:1093691..1098446,7	MCF-7	breast:
3	chr10:1032460..1036223-chr10:1037053..1039174,5	K562	blood:
4	chr10:1037288..1039582-chr10:1100848..1103600,2	K562	blood:
5	chr10:1037105..1042640-chr10:1092491..1096899,6	K562	blood:
6	chr10:993403..996250-chr10:1036309..1038565,2	K562	blood:
7	chr10:1036759..1038739-chr10:1058886..1061197,2	MCF-7	breast:
8	chr10:974439..980732-chr10:1030011..1038533,28	MCF-7	breast:
9	chr10:1037199..1043943-chr10:1053362..1060206,13	K562	blood:
10	chr10:1037105..1038655-chr10:1093115..1095926,2	K562	blood:
11	chr10:1024264..1026844-chr10:1037522..1040068,2	MCF-7	breast:
12	chr10:974510..978997-chr10:1037469..1040062,8	K562	blood:
13	chr10:974510..978091-chr10:1036448..1040062,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000067064	Chromatin interaction
ENSG00000047056	Chromatin interaction
ENSG00000229869	Chromatin interaction
ENSG00000107929	Chromatin interaction
ENSG00000107937	Chromatin interaction
ENSG00000205740	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1013504	1.00[ASN][1000 genomes]
rs10508206	0.83[CEU][hapmap]
rs10903358	1.00[ASN][1000 genomes]
rs11250228	1.00[CEU][hapmap]
rs11253504	1.00[ASN][1000 genomes]
rs11253518	1.00[ASN][1000 genomes]
rs11253530	1.00[ASN][1000 genomes]
rs11253537	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253538	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253539	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253540	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253549	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253550	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253557	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253558	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253559	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253560	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354914	1.00[ASN][1000 genomes]
rs12356612	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357633	1.00[ASN][1000 genomes]
rs12359796	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250891	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761180	1.00[ASN][1000 genomes]
rs12762228	1.00[ASN][1000 genomes]
rs12762955	0.83[CEU][hapmap]
rs12768348	1.00[ASN][1000 genomes]
rs12769002	1.00[ASN][1000 genomes]
rs12770173	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12770910	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12771179	1.00[ASN][1000 genomes]
rs12771539	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772979	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773961	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774985	1.00[ASN][1000 genomes]
rs12777021	1.00[ASN][1000 genomes]
rs12777788	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12777800	1.00[ASN][1000 genomes]
rs12777801	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778271	1.00[ASN][1000 genomes]
rs12781329	1.00[ASN][1000 genomes]
rs17221456	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221491	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs17293580	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17293608	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871621	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871622	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28512382	1.00[ASN][1000 genomes]
rs34115136	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34159706	1.00[ASN][1000 genomes]
rs34251037	1.00[ASN][1000 genomes]
rs34270668	1.00[ASN][1000 genomes]
rs34318754	1.00[ASN][1000 genomes]
rs34480046	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34487581	1.00[ASN][1000 genomes]
rs34527494	1.00[ASN][1000 genomes]
rs34885925	1.00[ASN][1000 genomes]
rs34982663	1.00[ASN][1000 genomes]
rs35028518	1.00[ASN][1000 genomes]
rs35306767	1.00[ASN][1000 genomes]
rs35363972	1.00[ASN][1000 genomes]
rs35443149	1.00[ASN][1000 genomes]
rs35666723	1.00[ASN][1000 genomes]
rs35667562	1.00[ASN][1000 genomes]
rs35670857	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35709890	1.00[ASN][1000 genomes]
rs35957139	1.00[ASN][1000 genomes]
rs41260144	1.00[ASN][1000 genomes]
rs55697724	1.00[ASN][1000 genomes]
rs55708963	1.00[ASN][1000 genomes]
rs55742421	1.00[ASN][1000 genomes]
rs56222464	1.00[ASN][1000 genomes]
rs61830900	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	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66797613	1.00[ASN][1000 genomes]
rs67205460	1.00[ASN][1000 genomes]
rs67696450	1.00[ASN][1000 genomes]
rs7088956	1.00[ASN][1000 genomes]
rs7093665	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094031	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72778228	1.00[ASN][1000 genomes]
rs7914758	1.00[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	esv2753756	chr10:985264-1052950	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	esv1812809	chr10:1021156-1051728	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
19	esv1813158	chr10:1021156-1062915	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
20	esv1831483	chr10:1021156-1062915	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
21	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
22	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17221463	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1035000-1038800	Weak transcription	Aorta	Aorta
2	chr10:1035000-1094000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:1035400-1039000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:1035400-1040000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr10:1035400-1040400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:1035600-1038400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr10:1035600-1038800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:1035600-1039000	Weak transcription	Fetal Kidney	kidney
9	chr10:1035600-1043600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:1035800-1038600	Weak transcription	Brain Angular Gyrus	brain
11	chr10:1035800-1038600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr10:1035800-1038600	Weak transcription	NHLF	lung
13	chr10:1035800-1038800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr10:1035800-1038800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:1035800-1038800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr10:1035800-1038800	Weak transcription	Brain Substantia Nigra	brain
17	chr10:1035800-1038800	Weak transcription	HSMMtube	muscle
18	chr10:1035800-1046800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr10:1035800-1066200	Strong transcription	NH-A	brain
20	chr10:1036000-1038400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr10:1036000-1038400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr10:1036000-1038400	Weak transcription	Primary T cells from cord blood	blood
23	chr10:1036000-1038400	Weak transcription	Adipose Nuclei	Adipose
24	chr10:1036000-1038400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr10:1036000-1038400	Weak transcription	Brain Germinal Matrix	brain
26	chr10:1036000-1038400	Weak transcription	Placenta	Placenta
27	chr10:1036000-1038400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:1036000-1038600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:1036000-1038600	Weak transcription	Fetal Thymus	thymus
30	chr10:1036000-1038600	Weak transcription	NHDF-Ad	bronchial
31	chr10:1036000-1038800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr10:1036000-1038800	Weak transcription	Brain Anterior Caudate	brain
33	chr10:1036000-1038800	Weak transcription	Brain Hippocampus Middle	brain
34	chr10:1036000-1038800	Weak transcription	Colonic Mucosa	Colon
35	chr10:1036000-1038800	Weak transcription	Esophagus	oesophagus
36	chr10:1036000-1038800	Weak transcription	Fetal Brain Male	brain
37	chr10:1036000-1038800	Weak transcription	Fetal Intestine Large	intestine
38	chr10:1036000-1038800	Weak transcription	Fetal Intestine Small	intestine
39	chr10:1036000-1038800	Weak transcription	Fetal Muscle Leg	muscle
40	chr10:1036000-1038800	Weak transcription	Fetal Stomach	stomach
41	chr10:1036000-1038800	Weak transcription	Ovary	ovary
42	chr10:1036000-1038800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr10:1036000-1038800	Weak transcription	Right Ventricle	heart
44	chr10:1036000-1038800	Weak transcription	Thymus	Thymus
45	chr10:1036000-1040400	Weak transcription	Colon Smooth Muscle	Colon
46	chr10:1036000-1040600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr10:1036000-1040600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr10:1036000-1040800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr10:1036000-1041000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr10:1036000-1046600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links