Variant report

Variant	rs2341889
Chromosome Location	chr14:56049204-56049205
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr14:56049179-56049313	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr14:56049017-56049412	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr14:56049147-56049377	HUVEC	blood vessel:	n/a	n/a
4	E2F4	chr14:56049084-56049375	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr14:56049104-56049393	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:56045115..56047584-chr14:56049131..56050750,2	K562	blood:
2	chr14:56047768..56050679-chr14:56060569..56062105,2	K562	blood:
3	chr14:56047540..56051954-chr14:56053859..56059782,6	K562	blood:
4	chr14:55946573..55948131-chr14:56047906..56049458,2	K562	blood:
5	chr14:56048425..56050750-chr14:56067419..56069440,2	MCF-7	breast:
6	chr14:56046559..56049206-chr14:56078372..56080917,2	MCF-7	breast:

No data

Variant related genes	Relation type
KTN1-AS1	TF binding region
ENSG00000186615	Chromatin interaction
ENSG00000126777	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10146870	0.86[ASN][1000 genomes]
rs10483644	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10483649	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12432588	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12432887	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12433592	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12434624	0.86[EUR][1000 genomes]
rs12434660	0.86[EUR][1000 genomes]
rs12434799	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12435643	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12587700	0.80[EUR][1000 genomes]
rs12587705	0.85[EUR][1000 genomes]
rs12589864	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12589867	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12590388	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12590936	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12882850	0.84[ASN][1000 genomes]
rs12888809	0.86[EUR][1000 genomes]
rs12895070	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12897227	0.85[ASN][1000 genomes]
rs17128610	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128614	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128655	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17128657	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17128677	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17128684	0.82[EUR][1000 genomes]
rs17128690	0.80[EUR][1000 genomes]
rs1951889	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1951890	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2093800	0.85[ASN][1000 genomes]
rs2252189	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2274076	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2274078	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2274079	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28458791	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28703642	0.83[EUR][1000 genomes]
rs34023572	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34111199	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34118806	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34184813	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34408323	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34548095	0.80[EUR][1000 genomes]
rs34697059	0.82[EUR][1000 genomes]
rs34709110	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34931260	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35047443	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35094494	0.87[EUR][1000 genomes]
rs35420484	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35451981	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35531912	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35535838	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35560341	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35790844	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4457912	0.93[ASN][1000 genomes]
rs55760841	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56229542	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60233569	0.80[EUR][1000 genomes]
rs61381603	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68127620	0.83[ASN][1000 genomes]
rs7154548	0.85[ASN][1000 genomes]
rs7156566	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72719463	0.91[ASN][1000 genomes]
rs8006443	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8007183	0.86[ASN][1000 genomes]
rs8007832	0.84[ASN][1000 genomes]
rs8008764	0.86[ASN][1000 genomes]
rs8011252	0.86[ASN][1000 genomes]
rs8015588	0.82[EUR][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56045200-56050000	Active TSS	GM12878-XiMat	blood
2	chr14:56045600-56050000	Active TSS	Right Atrium	heart
3	chr14:56045600-56051000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr14:56047600-56050000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr14:56047800-56049400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:56047800-56049800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:56048200-56050600	Weak transcription	Aorta	Aorta
8	chr14:56048200-56054200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr14:56048200-56068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:56048400-56050400	Weak transcription	Placenta	Placenta
11	chr14:56048400-56050600	Weak transcription	Pancreas	Pancrea
12	chr14:56048400-56050800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr14:56048400-56052000	Enhancers	Primary B cells from peripheral blood	blood
14	chr14:56048400-56052800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:56048400-56055200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr14:56048400-56056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr14:56048400-56068400	Weak transcription	Esophagus	oesophagus
18	chr14:56048400-56086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr14:56048600-56049400	Enhancers	Primary B cells from cord blood	blood
20	chr14:56048600-56049400	Weak transcription	Fetal Lung	lung
21	chr14:56048600-56049400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr14:56048600-56049600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:56048600-56049600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:56048600-56049600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr14:56048600-56049600	Weak transcription	Fetal Intestine Small	intestine
26	chr14:56048600-56049600	Enhancers	HUVEC	blood vessel
27	chr14:56048600-56049800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr14:56048600-56049800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr14:56048600-56049800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:56048600-56049800	Weak transcription	Fetal Kidney	kidney
31	chr14:56048600-56049800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr14:56048600-56050400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr14:56048600-56050400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr14:56048600-56050400	Weak transcription	Brain Angular Gyrus	brain
35	chr14:56048600-56050400	Weak transcription	Fetal Muscle Leg	muscle
36	chr14:56048600-56050400	Weak transcription	Ovary	ovary
37	chr14:56048600-56050400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr14:56048600-56050400	Weak transcription	Small Intestine	intestine
39	chr14:56048600-56050600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr14:56048600-56050600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr14:56048600-56050600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr14:56048600-56050600	Enhancers	Duodenum Mucosa	Duodenum
43	chr14:56048600-56050600	Weak transcription	Gastric	stomach
44	chr14:56048600-56050600	Weak transcription	Psoas Muscle	Psoas
45	chr14:56048600-56050600	Weak transcription	Spleen	Spleen
46	chr14:56048600-56050800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr14:56048600-56050800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr14:56048600-56050800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr14:56048600-56050800	Weak transcription	Colonic Mucosa	Colon
50	chr14:56048600-56050800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links