Variant report

Variant	rs10142739
Chromosome Location	chr14:56044061-56044062
allele	C/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	STAT3	chr14:56044015-56044375	MCF10A-Er-Src	breast:	n/a	chr14:56044134-56044142 chr14:56044161-56044172 chr14:56044163-56044171 chr14:56044074-56044085
2	JUND	chr14:56043829-56044403	MCF-7	breast:	n/a	n/a
3	EBF1	chr14:56044043-56044200	GM12878	blood:	n/a	n/a
4	GATA3	chr14:56043903-56044301	T-47D	breast:	n/a	n/a
5	ZNF143	chr14:56044026-56044216	GM12878	blood:	n/a	n/a
6	GATA2	chr14:56043899-56044292	HUVEC	blood vessel:	n/a	n/a
7	GATA3	chr14:56043797-56044437	SK-N-SH	brain:	n/a	n/a
8	SPI1	chr14:56043875-56044208	GM12891	blood:	n/a	n/a
9	BATF	chr14:56043978-56044311	GM12878	blood:	n/a	n/a
10	GATA3	chr14:56043717-56044477	SK-N-SH	brain:	n/a	n/a
11	RUNX3	chr14:56043847-56044365	GM12878	blood:	n/a	n/a
12	BATF	chr14:56043978-56044256	GM12878	blood:	n/a	n/a
13	EP300	chr14:56044011-56044298	GM12878	blood:	n/a	chr14:56044076-56044090
14	SPI1	chr14:56043887-56044237	GM12891	blood:	n/a	n/a
15	FOSL2	chr14:56043917-56044343	MCF-7	breast:	n/a	n/a
16	TCF12	chr14:56043776-56044393	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr14:56043795-56044384	MCF-7	breast:	n/a	n/a
18	FOXM1	chr14:56043926-56044371	GM12878	blood:	n/a	n/a
19	STAT3	chr14:56044029-56044325	MCF10A-Er-Src	breast:	n/a	chr14:56044134-56044142 chr14:56044161-56044172 chr14:56044163-56044171 chr14:56044074-56044085
20	GATA3	chr14:56043647-56044660	MCF-7	breast:	n/a	chr14:56044608-56044616
21	NFIC	chr14:56043791-56044353	GM12878	blood:	n/a	n/a
22	FOS	chr14:56044030-56044282	MCF10A-Er-Src	breast:	n/a	n/a
23	IKZF1	chr14:56043905-56044363	GM12878	blood:	n/a	n/a
24	RUNX3	chr14:56043964-56044280	GM12878	blood:	n/a	n/a
25	IRF4	chr14:56043912-56044313	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56037803..56044083-chr14:56044253..56047931,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBPL2-1	chr14:56042905-56044097	ENSG00000186615
2	lnc-TBPL2-1	chr14:56042875-56044097	ENSG00000186615
3	lnc-TBPL2-1	chr14:56042876-56044097	XLOC_011036
4	lnc-TBPL2-1	chr14:56042904-56044097	ENSG00000186615.6

Variant related genes	Relation type
KTN1	TF binding region
ENSG00000186615	Chromatin interaction
ENSG00000126777	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10140432	0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12100753	0.82[YRI][hapmap]
rs28656140	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56023600-56045200	Weak transcription	Primary T cells from cord blood	blood
2	chr14:56024200-56045400	Weak transcription	Adipose Nuclei	Adipose
3	chr14:56024400-56045200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr14:56024400-56045200	Weak transcription	Ovary	ovary
5	chr14:56024400-56045400	Weak transcription	Hela-S3	cervix
6	chr14:56024400-56045400	Weak transcription	Osteobl	bone
7	chr14:56024400-56045800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:56024600-56045400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:56025200-56045600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr14:56025800-56045400	Weak transcription	Fetal Muscle Leg	muscle
11	chr14:56026200-56045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:56028000-56044600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr14:56034200-56046000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:56035600-56045800	Weak transcription	Aorta	Aorta
15	chr14:56037000-56045600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr14:56037400-56045600	Weak transcription	Fetal Kidney	kidney
17	chr14:56037800-56045600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr14:56038400-56045200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr14:56038400-56045200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:56038600-56045000	Weak transcription	HSMMtube	muscle
21	chr14:56038600-56045200	Weak transcription	Brain Substantia Nigra	brain
22	chr14:56039000-56045800	Weak transcription	Primary B cells from cord blood	blood
23	chr14:56039200-56045400	Weak transcription	Right Atrium	heart
24	chr14:56039200-56045400	Weak transcription	HMEC	breast
25	chr14:56039600-56045000	Weak transcription	Brain Anterior Caudate	brain
26	chr14:56039600-56045200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr14:56039600-56045200	Weak transcription	Fetal Lung	lung
28	chr14:56039600-56045400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr14:56039600-56045400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:56039600-56045400	Weak transcription	Fetal Stomach	stomach
31	chr14:56039600-56045800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr14:56039800-56045000	Weak transcription	Brain Angular Gyrus	brain
33	chr14:56039800-56045000	Weak transcription	Fetal Brain Male	brain
34	chr14:56039800-56045200	Weak transcription	Brain Hippocampus Middle	brain
35	chr14:56039800-56045200	Weak transcription	NH-A	brain
36	chr14:56039800-56045400	Weak transcription	K562	blood
37	chr14:56039800-56045600	Weak transcription	Pancreas	Pancrea
38	chr14:56040000-56045000	Weak transcription	A549	lung
39	chr14:56040000-56045400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr14:56040200-56045200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr14:56040400-56045400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr14:56041000-56045600	Weak transcription	Fetal Intestine Small	intestine
43	chr14:56041200-56045800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr14:56041600-56045200	Weak transcription	Dnd41	blood
45	chr14:56041800-56045800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:56042000-56045200	Weak transcription	Colon Smooth Muscle	Colon
47	chr14:56042000-56045800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr14:56042000-56045800	Weak transcription	Gastric	stomach
49	chr14:56042000-56045800	Weak transcription	Lung	lung
50	chr14:56042200-56045400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links