Variant report

Variant	rs6013875
Chromosome Location	chr20:52656943-52656944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
2	chr20:52655188..52657937-chr20:55839006..55840900,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16998844	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2214529	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs406691	0.85[CEU][hapmap]
rs6013858	0.85[CEU][hapmap]
rs6013862	0.85[CEU][hapmap]
rs6013864	0.85[CEU][hapmap]
rs6013866	0.85[CEU][hapmap]
rs6013867	0.85[CEU][hapmap]
rs6013874	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6013877	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6013878	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6022892	0.85[CEU][hapmap]
rs6022893	0.82[CEU][hapmap]
rs6022896	0.82[CEU][hapmap]
rs6022903	0.82[CEU][hapmap]
rs6022905	0.85[CEU][hapmap]
rs6022906	0.85[CEU][hapmap]
rs6022907	0.85[CEU][hapmap]
rs6022908	0.85[CEU][hapmap]
rs6022909	0.82[CEU][hapmap]
rs6022920	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6022922	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6022934	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6097705	0.85[CEU][hapmap]
rs878868	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:82 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
3	esv2763673	chr20:52637074-52668126	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv3419	chr20:52637581-52672115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
5	nsv1064465	chr20:52643155-52658639	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv437187	chr20:52644514-52660120	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv1058315	chr20:52644518-52658639	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv1064456	chr20:52644721-52658639	Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv1055799	chr20:52644770-52657717	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv1059551	chr20:52644770-52658639	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv1067222	chr20:52644856-52658061	Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv1060500	chr20:52644856-52658639	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv1065821	chr20:52644856-52662562	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
14	nsv912939	chr20:52646029-52660741	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv912940	chr20:52646029-52663409	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
16	esv3513136	chr20:52646045-52659093	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
17	esv3513133	chr20:52646370-52658993	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
18	esv3513132	chr20:52646668-52658237	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
19	esv3454655	chr20:52646917-52658133	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
20	nsv586235	chr20:52646926-52657797	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
21	nsv586236	chr20:52646926-52658001	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
22	nsv517164	chr20:52646926-52660741	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv912941	chr20:52646926-52660741	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
24	nsv912942	chr20:52646926-52663409	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
25	esv3513138	chr20:52646952-52658112	Weak transcription Enhancers	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
26	esv3513135	chr20:52646964-52658088	Weak transcription Enhancers	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
27	esv3454654	chr20:52646970-52658079	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
28	esv3513139	chr20:52646987-52658036	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
29	esv3513137	chr20:52646999-52658057	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
30	esv3513134	chr20:52647007-52658053	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
31	esv3454656	chr20:52647065-52658009	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
32	esv3513141	chr20:52647065-52658009	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
33	esv13873	chr20:52647106-52658080	Weak transcription Enhancers	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
34	nsv1055315	chr20:52647808-52658061	Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
35	nsv1064515	chr20:52647808-52658561	Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
36	nsv1059526	chr20:52647808-52658639	Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
37	esv2421391	chr20:52647808-52658651	Weak transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
38	nsv442485	chr20:52647808-52658651	Weak transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
39	nsv1059343	chr20:52647808-52662562	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
40	nsv1065004	chr20:52647808-52665631	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
41	esv2760671	chr20:52647808-52665643	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
42	nsv1055891	chr20:52647808-52666885	Enhancers Strong transcription Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
43	nsv1067336	chr20:52647808-52668126	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
44	nsv1065888	chr20:52647808-52670378	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
45	nsv586244	chr20:52647823-52657797	Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
46	nsv586245	chr20:52647823-52658001	Weak transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
47	nsv586246	chr20:52647823-52660741	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
48	nsv586247	chr20:52647823-52663409	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
49	nsv433324	chr20:52647823-52663783	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
50	nsv586248	chr20:52647823-52663783	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
2	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52646000-52657000	Weak transcription	Gastric	stomach
5	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:52655200-52657200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:52655200-52658200	Enhancers	Fetal Stomach	stomach
8	chr20:52656800-52657200	Enhancers	Colon Smooth Muscle	Colon
9	chr20:52656800-52657400	Enhancers	Fetal Kidney	kidney
10	chr20:52656800-52657400	Enhancers	K562	blood

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