Variant report

Variant	rs11250238
Chromosome Location	chr10:1089616-1089617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr10:1089535-1089987	GM12878	blood:	n/a	n/a
2	MTA3	chr10:1089282-1090581	GM12878	blood:	n/a	n/a
3	CCNT2	chr10:1089325-1089679	K562	blood:	n/a	n/a
4	POLR2A	chr10:1089420-1089956	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:1088970-1092654	PBDE	blood:	n/a	n/a
6	POLR2A	chr10:1089578-1090001	HepG2	liver:	n/a	n/a
7	EP300	chr10:1089555-1090005	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:1089350-1092506	A549	lung:	n/a	n/a
9	POLR2A	chr10:1089372-1090500	GM12892	blood:	n/a	n/a
10	MAX	chr10:1089425-1089949	GM12878	blood:	n/a	n/a
11	PAX5	chr10:1089594-1089969	GM12878	blood:	n/a	n/a
12	TBP	chr10:1089540-1090078	GM12878	blood:	n/a	n/a
13	MXI1	chr10:1089538-1090049	GM12878	blood:	n/a	n/a
14	POLR2A	chr10:1089599-1089999	GM12891	blood:	n/a	n/a
15	ELF1	chr10:1089364-1090149	GM12878	blood:	n/a	n/a
16	WRNIP1	chr10:1089397-1090481	GM12878	blood:	n/a	n/a
17	POLR2A	chr10:1089458-1091279	Hela-S3	cervix:	n/a	n/a
18	NFATC1	chr10:1089315-1091460	GM12878	blood:	n/a	n/a
19	POLR2A	chr10:1082282-1092534	K562	blood:	n/a	n/a
20	BCLAF1	chr10:1089332-1090130	GM12878	blood:	n/a	n/a
21	POLR2A	chr10:1088869-1090278	PFSK-1	brain:	n/a	n/a
22	PAX5	chr10:1089370-1090085	GM12878	blood:	n/a	n/a
23	POLR2A	chr10:1089341-1090410	GM12878	blood:	n/a	n/a
24	POLR2A	chr10:1089372-1090091	GM12892	blood:	n/a	n/a
25	YY1	chr10:1089400-1089964	GM12878	blood:	n/a	n/a
26	POLR2A	chr10:1089336-1089687	K562	blood:	n/a	n/a
27	POLR2A	chr10:1089306-1091269	HepG2	liver:	n/a	n/a
28	POLR2A	chr10:1089448-1090107	GM12891	blood:	n/a	n/a
29	POLR2A	chr10:1089490-1089638	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr10:1089505-1089988	GM12878	blood:	n/a	n/a
31	POLR2A	chr10:1089337-1090560	GM19099	blood:	n/a	n/a
32	POLR2A	chr10:1089429-1089848	GM12878	blood:	n/a	n/a
33	RUNX3	chr10:1089451-1090031	GM12878	blood:	n/a	n/a
34	POLR2A	chr10:1089268-1090059	HL-60	blood:	n/a	n/a
35	POLR2A	chr10:1088828-1092481	MCF10A-Er-Src	breast:	n/a	n/a
36	SPI1	chr10:1089355-1089980	GM12878	blood:	n/a	n/a
37	JUND	chr10:1089585-1089627	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr10:1089311-1090737	GM12892	blood:	n/a	n/a
39	POLR2A	chr10:1089187-1089759	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr10:1088966-1092589	IMR90	lung:	n/a	n/a
41	PAX5	chr10:1089559-1090033	GM12878	blood:	n/a	n/a
42	RUNX3	chr10:1089299-1090077	GM12878	blood:	n/a	n/a
43	NFATC1	chr10:1089506-1090630	GM12878	blood:	n/a	n/a
44	POLR2A	chr10:1089355-1090015	GM12892	blood:	n/a	n/a
45	POLR2A	chr10:1089422-1089776	Hela-S3	cervix:	n/a	n/a
46	PML	chr10:1089403-1090168	GM12878	blood:	n/a	n/a
47	POLR2A	chr10:1089106-1090444	GM12878	blood:	n/a	n/a
48	POLR2A	chr10:1089472-1090077	GM12891	blood:	n/a	n/a
49	CTCF	chr10:1089580-1089730	GM12872	blood:	n/a	n/a
50	POLR2A	chr10:1089574-1091714	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:1086551..1092852-chr10:1093358..1097808,14	MCF-7	breast:
2	chr10:1082336..1085683-chr10:1088908..1090721,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTPBP4-1	chr10:1089469-1089623	ENSG00000232656.3

No data

Variant related genes	Relation type
RNU7-163P	TF binding region
ENSG00000047056	Chromatin interaction
ENSG00000067064	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10508205	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10737004	1.00[CHB][hapmap]
rs10795303	0.85[CHB][hapmap]
rs10795306	1.00[CHB][hapmap]
rs10904597	1.00[CHB][hapmap]
rs11250222	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs11250229	1.00[EUR][1000 genomes]
rs11250232	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs11253536	1.00[CHB][hapmap];0.80[GIH][hapmap]
rs11253552	1.00[CHB][hapmap];0.80[GIH][hapmap]
rs1135416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11592211	1.00[EUR][1000 genomes]
rs11599483	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1871628	0.85[YRI][hapmap]
rs1904671	1.00[CHB][hapmap]
rs2306405	0.85[EUR][1000 genomes]
rs2387213	1.00[CHB][hapmap]
rs2620942	1.00[CHB][hapmap]
rs3207775	1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs3793778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4403737	0.83[YRI][hapmap]
rs4880758	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4880759	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4880762	0.86[YRI][hapmap]
rs4880764	0.86[YRI][hapmap]
rs6560863	1.00[CHB][hapmap]
rs7071817	0.92[YRI][hapmap]
rs7076107	1.00[CHB][hapmap]
rs7080072	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7093383	0.81[ASN][1000 genomes]
rs7095853	0.85[CHB][hapmap]

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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1035000-1094000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:1060000-1091600	Weak transcription	Hela-S3	cervix
3	chr10:1063200-1092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:1073400-1091800	Weak transcription	Fetal Heart	heart
5	chr10:1082000-1089800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:1082400-1089800	Strong transcription	Brain Germinal Matrix	brain
7	chr10:1082400-1090200	Strong transcription	Fetal Intestine Large	intestine
8	chr10:1082600-1089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:1082600-1090000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr10:1082600-1094000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:1082800-1090200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:1083000-1090000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:1083000-1090400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:1083200-1090400	Strong transcription	NH-A	brain
15	chr10:1083400-1089800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:1083400-1090000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:1083400-1092000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr10:1083600-1090200	Weak transcription	Small Intestine	intestine
19	chr10:1083800-1090200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr10:1083800-1090400	Strong transcription	NHLF	lung
21	chr10:1084000-1090200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr10:1084000-1090200	Weak transcription	Right Ventricle	heart
23	chr10:1084000-1091600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr10:1084000-1093400	Weak transcription	Aorta	Aorta
25	chr10:1084200-1093400	Weak transcription	Thymus	Thymus
26	chr10:1084400-1091000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:1085000-1091200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr10:1085200-1090000	Strong transcription	HMEC	breast
29	chr10:1085200-1090800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr10:1085200-1090800	Strong transcription	HSMM	muscle
31	chr10:1085200-1091400	Weak transcription	Spleen	Spleen
32	chr10:1085400-1090000	Strong transcription	Fetal Lung	lung
33	chr10:1085400-1090200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:1085600-1090000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:1085800-1090000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:1086000-1090200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr10:1086200-1089800	Strong transcription	HepG2	liver
38	chr10:1087000-1090000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:1087000-1092200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr10:1087600-1090200	Weak transcription	Brain Hippocampus Middle	brain
41	chr10:1087600-1091400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:1087800-1089800	Strong transcription	Colonic Mucosa	Colon
43	chr10:1087800-1089800	Strong transcription	Fetal Intestine Small	intestine
44	chr10:1087800-1089800	Strong transcription	Ovary	ovary
45	chr10:1087800-1089800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr10:1087800-1090200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:1087800-1090200	Strong transcription	Fetal Stomach	stomach
48	chr10:1087800-1090400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr10:1088000-1093400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr10:1088200-1090000	Strong transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links