Variant report

Variant	rs12260310
Chromosome Location	chr10:38145932-38145933
allele	A/G
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	NRF1	chr10:38145877-38147306	SK-N-SH	brain:	n/a	chr10:38146624-38146635 chr10:38146594-38146605 chr10:38146592-38146606 chr10:38146595-38146609 chr10:38146595-38146604 chr10:38146621-38146635 chr10:38146624-38146635 chr10:38146595-38146606
2	POLR2A	chr10:38145898-38147194	PBDE	blood:	n/a	n/a
3	GATA1	chr10:38145595-38147205	PBDE	blood:	n/a	n/a
4	POLR2A	chr10:38145905-38147542	GM12892	blood:	n/a	n/a
5	RCOR1	chr10:38145743-38146975	K562	blood:	n/a	n/a
6	POLR2A	chr10:38145896-38147504	GM18951	blood:	n/a	n/a
7	RCOR1	chr10:38145627-38147274	K562	blood:	n/a	n/a
8	POLR2A	chr10:38145893-38147452	K562	blood:	n/a	n/a
9	HCFC1	chr10:38145882-38146046	K562	blood:	n/a	n/a
10	POLR2A	chr10:38145726-38147548	HepG2	liver:	n/a	n/a
11	POLR2A	chr10:38145870-38147267	GM19193	blood:	n/a	n/a
12	EP300	chr10:38145743-38146080	K562	blood:	n/a	n/a
13	TBL1XR1	chr10:38145648-38146027	K562	blood:	n/a	n/a
14	NR2F2	chr10:38145638-38146148	K562	blood:	n/a	n/a
15	UBTF	chr10:38145791-38147270	K562	blood:	n/a	n/a
16	POLR2A	chr10:38145844-38147891	K562	blood:	n/a	n/a
17	HMGN3	chr10:38145758-38147295	K562	blood:	n/a	n/a
18	POLR2A	chr10:38145894-38147431	GM18505	blood:	n/a	n/a
19	MYC	chr10:38145803-38147172	K562	blood:	n/a	chr10:38146617-38146633
20	MXI1	chr10:38145806-38147213	GM12878	blood:	n/a	n/a
21	IRF1	chr10:38145335-38146014	K562	blood:	n/a	n/a
22	MAX	chr10:38145911-38147147	K562	blood:	n/a	chr10:38146617-38146633
23	KAP1	chr10:38145928-38147389	U2OS	brain:	n/a	n/a
24	POLR2A	chr10:38145703-38147442	K562	blood:	n/a	n/a
25	STAT5A	chr10:38145655-38146133	K562	blood:	n/a	n/a
26	ZC3H11A	chr10:38145826-38146094	K562	blood:	n/a	n/a
27	MYC	chr10:38145786-38147222	K562	blood:	n/a	chr10:38146617-38146633
28	ZNF263	chr10:38145788-38147406	HEK293-T-REx	kidney:	n/a	chr10:38146540-38146549
29	GATA2	chr10:38145726-38146107	K562	blood:	n/a	n/a
30	CHD2	chr10:38145864-38146136	K562	blood:	n/a	n/a
31	MAZ	chr10:38145826-38147202	K562	blood:	n/a	chr10:38146617-38146633
32	POLR2A	chr10:38145871-38147514	GM19099	blood:	n/a	n/a
33	NR2F2	chr10:38145581-38146878	K562	blood:	n/a	n/a
34	POLR2A	chr10:38145782-38146151	K562	blood:	n/a	n/a
35	MAZ	chr10:38145853-38147245	IMR90	lung:	n/a	chr10:38146617-38146633
36	HEY1	chr10:38145826-38146243	K562	blood:	n/a	n/a
37	JUND	chr10:38145794-38147114	K562	blood:	n/a	n/a
38	POLR2A	chr10:38145869-38147676	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr10:38145664-38147522	GM12891	blood:	n/a	n/a
40	CCNT2	chr10:38145723-38147210	K562	blood:	n/a	n/a
41	MXI1	chr10:38145207-38147932	SK-N-SH	brain:	n/a	n/a
42	ARID3A	chr10:38145868-38146862	HepG2	liver:	n/a	n/a
43	POLR2A	chr10:38145802-38147445	Raji	blood:	n/a	n/a
44	IRF1	chr10:38145789-38146075	K562	blood:	n/a	n/a
45	TAL1	chr10:38145692-38146191	K562	blood:	n/a	n/a
46	MXI1	chr10:38145819-38147816	IMR90	lung:	n/a	n/a
47	TBL1XR1	chr10:38145830-38146100	K562	blood:	n/a	n/a
48	WRNIP1	chr10:38145828-38147414	GM12878	blood:	n/a	n/a
49	BHLHE40	chr10:38145784-38147354	K562	blood:	n/a	n/a
50	TEAD4	chr10:38145714-38146095	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:38119569..38121189-chr10:38145461..38148334,3	MCF-7	breast:
2	chr10:38123782..38128970-chr10:38145175..38149505,4	MCF-7	breast:
3	chr10:38145904..38148087-chr9:86593901..86595485,2	MCF-7	breast:
4	chr10:38144757..38148220-chr10:38264242..38266228,3	MCF-7	breast:
5	chr10:38145545..38147887-chr10:38265015..38266536,2	MCF-7	breast:
6	chr10:38145553..38148128-chr10:38264831..38267581,3	K562	blood:
7	chr10:38125960..38130211-chr10:38145750..38148095,4	MCF-7	breast:
8	chr10:38145480..38148192-chr10:38381964..38384579,2	MCF-7	breast:
9	chr10:38144844..38146418-chr10:38148351..38151318,2	K562	blood:

Variant related genes	Relation type
ENSG00000236514	TF binding region
ENSG00000175395	Chromatin interaction
ENSG00000266800	Chromatin interaction
ENSG00000198105	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000226447	Chromatin interaction
ENSG00000075407	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10827821	0.82[AFR][1000 genomes]
rs10827830	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10827834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827838	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011332	0.82[AFR][1000 genomes]
rs11011356	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11011357	0.94[AFR][1000 genomes]
rs11011358	0.88[AFR][1000 genomes]
rs11011364	1.00[EUR][1000 genomes]
rs11011368	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11011375	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11011376	1.00[EUR][1000 genomes]
rs11011385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11011393	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011403	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011412	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011415	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011417	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11011428	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011429	1.00[EUR][1000 genomes]
rs11011430	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011438	1.00[EUR][1000 genomes]
rs11812927	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813932	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11814622	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11815775	0.82[AFR][1000 genomes]
rs11816307	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11816860	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11816995	0.94[AFR][1000 genomes]
rs11817696	1.00[EUR][1000 genomes]
rs11817782	0.82[AFR][1000 genomes]
rs11818933	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11819551	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12240311	1.00[EUR][1000 genomes]
rs12241614	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12242131	0.82[AFR][1000 genomes]
rs12242343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12244864	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12245586	1.00[EUR][1000 genomes]
rs12248857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12250395	1.00[EUR][1000 genomes]
rs12250465	0.82[AFR][1000 genomes]
rs12251570	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12252091	0.89[EUR][1000 genomes]
rs12252754	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12256181	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12256794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12256916	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12257632	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12257902	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12258024	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12258128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12258252	1.00[EUR][1000 genomes]
rs12260189	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12262559	1.00[EUR][1000 genomes]
rs12262814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12262927	1.00[EUR][1000 genomes]
rs12266728	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12267847	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12267923	1.00[EUR][1000 genomes]
rs12268435	0.82[AFR][1000 genomes]
rs12269398	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12761218	0.82[AFR][1000 genomes]
rs12770231	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12773340	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12777107	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12778900	1.00[EUR][1000 genomes]
rs12779056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12783599	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2023432	1.00[EUR][1000 genomes]
rs34152840	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34222428	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34445730	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34591573	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34724357	1.00[EUR][1000 genomes]
rs34918037	1.00[EUR][1000 genomes]
rs34964888	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35006520	1.00[EUR][1000 genomes]
rs35047448	0.82[AFR][1000 genomes]
rs35056062	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35246660	1.00[EUR][1000 genomes]
rs35404142	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35818588	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57753536	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60538050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71489160	0.82[AFR][1000 genomes]
rs71491203	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71491210	1.00[EUR][1000 genomes]
rs71491212	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71491214	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491223	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491227	1.00[EUR][1000 genomes]
rs71491228	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491229	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9651365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38143800-38146000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:38143800-38147400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr10:38144000-38147600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr10:38144200-38146800	Active TSS	Stomach Smooth Muscle	stomach
5	chr10:38144200-38147600	Active TSS	Right Atrium	heart
6	chr10:38144400-38146000	Flanking Active TSS	Osteobl	bone
7	chr10:38144400-38147200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:38144400-38147200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:38144400-38147200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:38144400-38147600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:38144400-38147800	Active TSS	NH-A	brain
12	chr10:38144600-38147600	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr10:38144600-38147600	Active TSS	Psoas Muscle	Psoas
14	chr10:38144600-38147600	Active TSS	A549	lung
15	chr10:38144800-38146000	Active TSS	Fetal Brain Female	brain
16	chr10:38144800-38146000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr10:38144800-38147200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:38144800-38147200	Active TSS	Brain Cingulate Gyrus	brain
19	chr10:38144800-38147200	Active TSS	Rectal Smooth Muscle	rectum
20	chr10:38144800-38147200	Active TSS	Thymus	Thymus
21	chr10:38144800-38147600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr10:38144800-38147600	Active TSS	Brain Germinal Matrix	brain
23	chr10:38144800-38147800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:38144800-38147800	Active TSS	Brain Anterior Caudate	brain
25	chr10:38144800-38147800	Active TSS	NHLF	lung
26	chr10:38145000-38146000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr10:38145000-38146000	Weak transcription	Stomach Mucosa	stomach
28	chr10:38145000-38147200	Active TSS	Brain Angular Gyrus	brain
29	chr10:38145000-38147200	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr10:38145200-38146400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:38145200-38146800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:38145200-38147400	Active TSS	Pancreas	Pancrea
33	chr10:38145200-38147600	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr10:38145200-38147600	Active TSS	Aorta	Aorta
35	chr10:38145400-38146000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr10:38145400-38146000	Weak transcription	Small Intestine	intestine
37	chr10:38145400-38146200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr10:38145400-38146400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr10:38145400-38147000	Active TSS	HMEC	breast
40	chr10:38145400-38147000	Active TSS	K562	blood
41	chr10:38145400-38147200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr10:38145400-38147200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:38145400-38147200	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr10:38145400-38147200	Active TSS	Fetal Kidney	kidney
45	chr10:38145400-38147200	Active TSS	Fetal Muscle Leg	muscle
46	chr10:38145400-38147200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr10:38145400-38147200	Active TSS	NHEK	skin
48	chr10:38145400-38147400	Active TSS	Left Ventricle	heart
49	chr10:38145400-38147400	Active TSS	Ovary	ovary
50	chr10:38145400-38147400	Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links