Variant report

Variant	rs2255967
Chromosome Location	chr10:43903919-43903920
allele	A/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	MXI1	chr10:43902185-43905112	HepG2	liver:	n/a	chr10:43904301-43904316
2	POLR2A	chr10:43901067-43905573	HL-60	blood:	n/a	n/a
3	MXI1	chr10:43902599-43905102	Hela-S3	cervix:	n/a	chr10:43904301-43904316
4	IRF1	chr10:43902895-43905077	K562	blood:	n/a	chr10:43904331-43904345 chr10:43904091-43904105 chr10:43904518-43904532 chr10:43904669-43904683 chr10:43904347-43904361 chr10:43903277-43903291
5	POLR2A	chr10:43903530-43904061	A549	lung:	n/a	n/a
6	TEAD4	chr10:43902955-43903985	K562	blood:	n/a	n/a
7	MAX	chr10:43902163-43905172	K562	blood:	n/a	chr10:43904307-43904316 chr10:43903332-43903343 chr10:43903333-43903342 chr10:43904402-43904411 chr10:43903767-43903774
8	PBX3	chr10:43902976-43904025	A549	lung:	n/a	n/a
9	HDAC2	chr10:43903579-43904732	K562	blood:	n/a	n/a
10	POLR2A	chr10:43901131-43905953	HepG2	liver:	n/a	n/a
11	JUN	chr10:43902090-43905336	K562	blood:	n/a	chr10:43902652-43902661 chr10:43904977-43904986
12	SMARCB1	chr10:43902578-43905702	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr10:43902530-43905094	HepG2	liver:	n/a	n/a
14	SETDB1	chr10:43903129-43905501	K562	blood:	n/a	chr10:43904422-43904446
15	NR2F2	chr10:43902718-43904036	K562	blood:	n/a	n/a
16	POLR2A	chr10:43902517-43905565	GM12891	blood:	n/a	n/a
17	SIN3AK20	chr10:43902854-43905693	HCT-116	colon:	n/a	n/a
18	POLR2A	chr10:43901150-43905187	K562	blood:	n/a	n/a
19	E2F6	chr10:43902545-43905260	K562	blood:	n/a	chr10:43903002-43903012 chr10:43904863-43904870 chr10:43902697-43902708 chr10:43904932-43904949 chr10:43904863-43904870 chr10:43902678-43902688 chr10:43902908-43902920 chr10:43902675-43902685 chr10:43904863-43904870 chr10:43904730-43904745 chr10:43904670-43904679
20	POLR2A	chr10:43900942-43905753	GM12878	blood:	n/a	n/a
21	MAX	chr10:43902831-43905956	HCT-116	colon:	n/a	chr10:43904307-43904316 chr10:43903332-43903343 chr10:43903333-43903342 chr10:43904402-43904411 chr10:43903767-43903774
22	WRNIP1	chr10:43903824-43903926	GM12878	blood:	n/a	n/a
23	POLR2A	chr10:43902445-43905122	GM12891	blood:	n/a	n/a
24	MAX	chr10:43903121-43905142	K562	blood:	n/a	chr10:43904307-43904316 chr10:43903332-43903343 chr10:43903333-43903342 chr10:43904402-43904411 chr10:43903767-43903774
25	MAX	chr10:43902453-43905428	A549	lung:	n/a	chr10:43904307-43904316 chr10:43903332-43903343 chr10:43903333-43903342 chr10:43904402-43904411 chr10:43903767-43903774
26	CEBPB	chr10:43902918-43903980	HCT-116	colon:	n/a	n/a
27	POLR2A	chr10:43902392-43905656	GM12892	blood:	n/a	n/a
28	ETS1	chr10:43902999-43904855	K562	blood:	n/a	chr10:43904758-43904769 chr10:43904668-43904679 chr10:43904616-43904625
29	POLR2A	chr10:43900620-43906464	MCF10A-Er-Src	breast:	n/a	n/a
30	TCF12	chr10:43902929-43905010	ECC-1	luminal epithelium:	n/a	chr10:43903008-43903018
31	MAX	chr10:43902835-43905112	NB4	blood:	n/a	chr10:43904307-43904316 chr10:43903332-43903343 chr10:43903333-43903342 chr10:43904402-43904411 chr10:43903767-43903774
32	HEY1	chr10:43902498-43905171	K562	blood:	n/a	chr10:43904665-43904680 chr10:43902997-43903012 chr10:43903011-43903026 chr10:43904668-43904683 chr10:43902676-43902691
33	CHD1	chr10:43901481-43905156	GM12878	blood:	n/a	chr10:43904759-43904769
34	TAL1	chr10:43902047-43905077	K562	blood:	n/a	n/a
35	POLR2A	chr10:43900975-43906126	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr10:43903640-43903922	U87	brain:	n/a	n/a
37	MXI1	chr10:43901128-43904565	K562	blood:	n/a	chr10:43901736-43901745 chr10:43904301-43904316 chr10:43901736-43901745
38	CTCF	chr10:43903419-43903983	K562	blood:	n/a	chr10:43903683-43903696 chr10:43903683-43903692
39	MAZ	chr10:43902177-43905136	IMR90	lung:	n/a	chr10:43904307-43904316 chr10:43903332-43903343 chr10:43903333-43903342 chr10:43904402-43904411 chr10:43903767-43903774
40	POLR2A	chr10:43902550-43905532	GM18526	blood:	n/a	n/a
41	POLR2A	chr10:43901128-43906303	GM12891	blood:	n/a	n/a
42	POLR2A	chr10:43901152-43906023	GM12878	blood:	n/a	n/a
43	POLR2A	chr10:43901249-43906054	K562	blood:	n/a	n/a
44	POLR2A	chr10:43900693-43905774	Hela-S3	cervix:	n/a	n/a
45	GATA3	chr10:43903913-43905095	A549	lung:	n/a	chr10:43904976-43904986
46	POLR2A	chr10:43902308-43905775	PBDE	blood:	n/a	n/a
47	MYC	chr10:43902515-43905218	Hela-S3	cervix:	n/a	chr10:43904307-43904316 chr10:43903332-43903343 chr10:43903333-43903342 chr10:43904402-43904411 chr10:43903767-43903774
48	POLR2A	chr10:43900254-43905917	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr10:43902809-43905630	GM12878	blood:	n/a	n/a
50	MAX	chr10:43902514-43904018	ECC-1	luminal epithelium:	n/a	chr10:43903332-43903343 chr10:43903333-43903342 chr10:43903767-43903774

No.	Distal block	Cell Line	Cell type
1	chr1:28834319..28834870-chr10:43903446..43904273,2	Hela-S3	cervix:
2	chr10:43867647..43875264-chr10:43900659..43906151,11	MCF-7	breast:
3	chr10:43902834..43905281-chr10:44101183..44103050,2	MCF-7	breast:
4	chr10:43903805..43904690-chr9:91925920..91926518,2	Hela-S3	cervix:
5	chr10:43901751..43904156-chr7:26239345..26241405,2	K562	blood:
6	chr10:43903162..43904071-chr16:68002331..68002833,2	Hela-S3	cervix:
7	chr10:43901370..43906375-chr10:43928042..43934083,16	MCF-7	breast:
8	chr10:43901784..43908257-chr10:43928243..43934263,17	MCF-7	breast:
9	chr10:43899870..43905980-chr10:43953401..43957689,7	MCF-7	breast:
10	chr10:43903427..43904398-chr20:43594621..43595269,2	Hela-S3	cervix:
11	chr10:43903244..43904543-chr10:43931320..43932838,6	Hela-S3	cervix:
12	chr10:43902635..43905319-chr11:65265113..65267204,2	K562	blood:
13	chr10:43901770..43904893-chr10:44100789..44103373,5	MCF-7	breast:
14	chr10:43696064..43699246-chr10:43901638..43904576,3	K562	blood:
15	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:
16	chr10:43696835..43700131-chr10:43902185..43905182,4	K562	blood:
17	chr10:43902596..43905009-chr12:7053130..7055096,2	K562	blood:

Variant related genes	Relation type
HNRNPF	TF binding region
ENSG00000252532	Chromatin interaction
ENSG00000123975	Chromatin interaction
ENSG00000101109	Chromatin interaction
ENSG00000198915	Chromatin interaction
ENSG00000232004	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000124067	Chromatin interaction
ENSG00000243660	Chromatin interaction
ENSG00000198298	Chromatin interaction
ENSG00000272173	Chromatin interaction
ENSG00000122566	Chromatin interaction
ENSG00000227477	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000122565	Chromatin interaction
ENSG00000150201	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10793431	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10899794	0.88[ASN][1000 genomes]
rs10899797	0.96[ASN][1000 genomes]
rs10899798	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10899799	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11238526	0.95[ASN][1000 genomes]
rs1126709	0.99[ASN][1000 genomes]
rs12257917	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416226	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2066043	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2066044	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2247860	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2247979	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247981	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2248332	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2248335	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2248469	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2248931	0.80[ASN][1000 genomes]
rs2250444	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252783	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2252785	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2252800	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252804	0.90[AFR][1000 genomes]
rs2256495	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2260200	0.82[AFR][1000 genomes]
rs2261636	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2265886	0.85[AFR][1000 genomes]
rs2265887	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2265888	0.81[AFR][1000 genomes]
rs2265952	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265953	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265954	0.82[AFR][1000 genomes]
rs2460558	0.88[ASN][1000 genomes]
rs2492404	0.85[ASN][1000 genomes]
rs2492405	0.84[AFR][1000 genomes]
rs2492407	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2492408	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2492409	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2492410	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2492411	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2492412	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2493648	0.82[AFR][1000 genomes]
rs2819032	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819034	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2946992	0.88[ASN][1000 genomes]
rs2999276	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2999282	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2999286	0.87[ASN][1000 genomes]
rs2999287	0.88[AFR][1000 genomes]
rs3000700	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4551711	0.80[AFR][1000 genomes]
rs4584528	0.84[AFR][1000 genomes]
rs4597022	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4948726	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56059584	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60739384	0.88[ASN][1000 genomes]
rs61859002	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6421744	0.80[AFR][1000 genomes]
rs7069214	0.82[AFR][1000 genomes]
rs7070029	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7088430	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7092599	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7894374	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7905676	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer 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	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825355	chr10:43890579-43923802	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
8	esv3395522	chr10:43903571-43906119	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43900200-43904600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr10:43900800-43905600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr10:43901000-43905800	Active TSS	HSMM	muscle
4	chr10:43901200-43904000	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr10:43901200-43904400	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr10:43901200-43905200	Active TSS	Small Intestine	intestine
7	chr10:43901200-43905800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:43901400-43905000	Active TSS	HMEC	breast
9	chr10:43901400-43905200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr10:43901400-43905400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr10:43901400-43905400	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr10:43901400-43905400	Active TSS	Ovary	ovary
13	chr10:43901400-43905600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr10:43901400-43905800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr10:43901600-43905400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr10:43901600-43905400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:43901600-43905400	Active TSS	Gastric	stomach
18	chr10:43901600-43905600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr10:43901600-43905600	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr10:43901600-43905600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr10:43901600-43905600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr10:43901600-43905600	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr10:43901600-43905600	Active TSS	Right Atrium	heart
24	chr10:43901600-43905600	Active TSS	GM12878-XiMat	blood
25	chr10:43901600-43905600	Active TSS	HSMMtube	muscle
26	chr10:43901600-43905600	Active TSS	NHDF-Ad	bronchial
27	chr10:43901600-43905600	Active TSS	NHLF	lung
28	chr10:43901600-43905800	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr10:43901600-43905800	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr10:43901600-43906000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:43901800-43905000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr10:43901800-43905000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:43901800-43905000	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr10:43901800-43905000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:43901800-43905200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr10:43901800-43905400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:43901800-43905400	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr10:43901800-43905400	Active TSS	Liver	Liver
39	chr10:43901800-43905400	Active TSS	Esophagus	oesophagus
40	chr10:43901800-43905400	Active TSS	Fetal Intestine Large	intestine
41	chr10:43901800-43905400	Active TSS	Fetal Intestine Small	intestine
42	chr10:43901800-43905400	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr10:43901800-43905400	Active TSS	Stomach Mucosa	stomach
44	chr10:43901800-43905400	Active TSS	Hela-S3	cervix
45	chr10:43901800-43905600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr10:43901800-43905600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:43901800-43905600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr10:43901800-43905800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr10:43901800-43905800	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr10:43901800-43905800	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links