Variant report

Variant	rs2892253
Chromosome Location	chr10:1032812-1032813
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	MYC	chr10:1032313-1033142	K562	blood:	n/a	chr10:1032547-1032556 chr10:1032548-1032557
2	SPI1	chr10:1032781-1033119	K562	blood:	n/a	chr10:1032966-1032979 chr10:1032965-1032978 chr10:1032968-1032977
3	POLR2A	chr10:1032737-1034966	K562	blood:	n/a	n/a
4	ZNF384	chr10:1032779-1033152	K562	blood:	n/a	n/a
5	SPI1	chr10:1032648-1033535	GM12878	blood:	n/a	chr10:1032966-1032979 chr10:1032965-1032978 chr10:1032968-1032977
6	MYC	chr10:1032135-1033109	MCF10A-Er-Src	breast:	n/a	chr10:1032547-1032556 chr10:1032548-1032557
7	SPI1	chr10:1032726-1033237	GM12891	blood:	n/a	chr10:1032966-1032979 chr10:1032965-1032978 chr10:1032968-1032977
8	RCOR1	chr10:1032172-1033211	K562	blood:	n/a	n/a
9	POLR2A	chr10:1032365-1032876	HepG2	liver:	n/a	n/a
10	POLR2A	chr10:1032776-1034962	K562	blood:	n/a	n/a
11	POLR2A	chr10:1032597-1033980	K562	blood:	n/a	n/a
12	SPI1	chr10:1032771-1033207	GM12891	blood:	n/a	chr10:1032966-1032979 chr10:1032965-1032978 chr10:1032968-1032977

No.	Distal block	Cell Line	Cell type
1	chr10:1030088..1034279-chr10:1100732..1103594,4	MCF-7	breast:
2	chr10:1019821..1022788-chr10:1029841..1033519,4	MCF-7	breast:
3	chr10:1010243..1012883-chr10:1030629..1033582,2	K562	blood:
4	chr10:975309..980832-chr10:1031626..1035973,12	K562	blood:
5	chr10:1032470..1034485-chr10:1092422..1096343,5	MCF-7	breast:
6	chr10:1015043..1019353-chr10:1030351..1034278,6	MCF-7	breast:
7	chr10:1031887..1035944-chr10:1099515..1103666,8	MCF-7	breast:
8	chr10:1031655..1033355-chr10:1053764..1056440,2	K562	blood:
9	chr10:974439..980732-chr10:1030011..1038533,28	MCF-7	breast:
10	chr10:976344..979673-chr10:1032747..1036349,14	K562	blood:
11	chr10:992595..994110-chr10:1032273..1033999,2	K562	blood:
12	chr10:1007049..1008640-chr10:1032331..1034053,2	K562	blood:
13	chr10:1015182..1016794-chr10:1031895..1033943,2	K562	blood:
14	chr10:1031711..1035740-chr10:1100728..1103796,4	K562	blood:
15	chr10:974636..980819-chr10:1029938..1037009,15	MCF-7	breast:

Variant related genes	Relation type
GTPBP4	TF binding region
ENSG00000047056	Chromatin interaction
ENSG00000229869	Chromatin interaction
ENSG00000067064	Chromatin interaction
ENSG00000107929	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10795304	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10795305	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10795307	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10904591	0.81[EUR][1000 genomes]
rs10904592	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10904593	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11253542	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11253543	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11253544	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11253564	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12217202	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12355506	0.86[EUR][1000 genomes]
rs2306408	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2892252	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3765102	0.93[EUR][1000 genomes]
rs5027030	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7071250	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7081516	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7082783	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7094916	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7097976	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7905827	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7917055	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7920922	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1024600-1033200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr10:1025400-1033000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:1026600-1033000	Weak transcription	Brain Hippocampus Middle	brain
4	chr10:1026800-1033000	Weak transcription	Liver	Liver
5	chr10:1026800-1033400	Weak transcription	Aorta	Aorta
6	chr10:1026800-1033400	Weak transcription	Lung	lung
7	chr10:1026800-1033400	Weak transcription	Ovary	ovary
8	chr10:1027200-1033000	Weak transcription	Primary T cells from cord blood	blood
9	chr10:1027400-1033000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr10:1027400-1033000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:1027400-1033200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr10:1027400-1033200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr10:1027400-1033200	Weak transcription	Fetal Muscle Leg	muscle
14	chr10:1027800-1033400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:1028000-1033000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:1028200-1033200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:1028200-1033200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr10:1028600-1033000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:1028600-1033000	Weak transcription	Brain Substantia Nigra	brain
20	chr10:1028800-1033200	Weak transcription	Brain Germinal Matrix	brain
21	chr10:1029000-1033000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr10:1029200-1033400	Enhancers	Fetal Intestine Large	intestine
23	chr10:1029200-1033400	Enhancers	Fetal Intestine Small	intestine
24	chr10:1029400-1033000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr10:1029400-1033200	Enhancers	Stomach Mucosa	stomach
26	chr10:1029400-1033200	Enhancers	HepG2	liver
27	chr10:1029600-1033000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr10:1030000-1033000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr10:1030000-1033400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr10:1030000-1033400	Weak transcription	Esophagus	oesophagus
31	chr10:1030400-1033400	Enhancers	Placenta	Placenta
32	chr10:1030600-1033400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:1030600-1033400	Weak transcription	Left Ventricle	heart
34	chr10:1030800-1033200	Enhancers	Fetal Lung	lung
35	chr10:1030800-1033400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:1031000-1033000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr10:1031000-1033000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr10:1031000-1033400	Enhancers	Hela-S3	cervix
39	chr10:1031400-1033000	Enhancers	NH-A	brain
40	chr10:1031600-1033000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr10:1031600-1033000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr10:1031600-1033000	Enhancers	A549	lung
43	chr10:1031600-1033000	Enhancers	HMEC	breast
44	chr10:1031600-1033200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:1031600-1033200	Enhancers	NHEK	skin
46	chr10:1031600-1033400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr10:1031800-1033000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr10:1031800-1033000	Weak transcription	Pancreas	Pancrea
49	chr10:1031800-1033200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr10:1031800-1033200	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links