Variant report

Variant	rs2892254
Chromosome Location	chr10:1098002-1098003
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:1097468-1098475	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:1093469-1098007	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:1094730..1096731-chr10:1096992..1098586,2	MCF-7	breast:
2	chr10:1090197..1098635-chr10:1098667..1108160,39	K562	blood:
3	chr10:1083077..1085466-chr10:1096305..1099633,3	MCF-7	breast:
4	chr10:1033990..1039615-chr10:1093691..1098446,7	MCF-7	breast:
5	chr10:1033680..1035425-chr10:1096903..1098612,2	MCF-7	breast:

Variant related genes	Relation type
IDI1	TF binding region
WDR37	TF binding region
ENSG00000107937	Chromatin interaction
ENSG00000205740	Chromatin interaction
ENSG00000047056	Chromatin interaction
ENSG00000067064	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10047269	0.96[ASN][1000 genomes]
rs10047382	0.84[ASN][1000 genomes]
rs10047383	0.85[ASN][1000 genomes]
rs10219038	0.96[ASN][1000 genomes]
rs11250242	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11250252	0.96[ASN][1000 genomes]
rs11815047	0.86[ASN][1000 genomes]
rs11819178	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11819230	0.91[ASN][1000 genomes]
rs12247779	0.87[ASN][1000 genomes]
rs12247818	0.98[ASN][1000 genomes]
rs12268949	0.96[ASN][1000 genomes]
rs12359250	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41299206	0.94[ASN][1000 genomes]
rs61571350	0.89[ASN][1000 genomes]
rs7071670	0.96[ASN][1000 genomes]
rs7075830	0.83[ASN][1000 genomes]
rs7093915	0.96[ASN][1000 genomes]
rs7100114	0.96[ASN][1000 genomes]
rs74120451	0.96[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	nsv894724	chr10:1084942-1116294	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2892254	IDI1	cis	brain	BrainEAC
rs2892254	IDI1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1095800-1102000	Weak transcription	Spleen	Spleen
2	chr10:1096000-1098200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:1096000-1098400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:1096000-1098600	Weak transcription	Ovary	ovary
5	chr10:1096000-1099600	Weak transcription	Pancreas	Pancrea
6	chr10:1096000-1101800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr10:1096000-1101800	Weak transcription	Gastric	stomach
8	chr10:1096200-1100800	Weak transcription	Aorta	Aorta
9	chr10:1096400-1098400	Weak transcription	Right Ventricle	heart
10	chr10:1096400-1098800	Genic enhancers	Brain Germinal Matrix	brain
11	chr10:1096600-1100000	Genic enhancers	Liver	Liver
12	chr10:1096800-1098200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr10:1096800-1098200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr10:1096800-1098200	Weak transcription	Brain Anterior Caudate	brain
15	chr10:1096800-1098200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:1096800-1098200	Enhancers	NHEK	skin
17	chr10:1096800-1098400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr10:1096800-1098600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr10:1096800-1098600	Weak transcription	Fetal Kidney	kidney
20	chr10:1096800-1098600	Weak transcription	Lung	lung
21	chr10:1096800-1098600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr10:1096800-1099400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:1096800-1099600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:1096800-1099600	Weak transcription	Colonic Mucosa	Colon
25	chr10:1096800-1099800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr10:1096800-1099800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:1096800-1099800	Weak transcription	Psoas Muscle	Psoas
28	chr10:1096800-1100000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:1096800-1100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:1096800-1100200	Strong transcription	Fetal Muscle Leg	muscle
31	chr10:1096800-1100400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr10:1096800-1100600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr10:1096800-1100800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr10:1096800-1100800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr10:1096800-1100800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr10:1096800-1100800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr10:1096800-1100800	Strong transcription	Fetal Thymus	thymus
38	chr10:1096800-1100800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr10:1096800-1100800	Weak transcription	Right Atrium	heart
40	chr10:1096800-1100800	Weak transcription	Small Intestine	intestine
41	chr10:1096800-1101600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:1096800-1101800	Weak transcription	Esophagus	oesophagus
43	chr10:1097000-1098200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr10:1097000-1098200	Strong transcription	Fetal Lung	lung
45	chr10:1097000-1099800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr10:1097000-1100200	Weak transcription	Colon Smooth Muscle	Colon
47	chr10:1097200-1098200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr10:1097200-1098200	Weak transcription	Adipose Nuclei	Adipose
49	chr10:1097200-1098400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:1097200-1098400	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links