Variant report

Variant	rs35005258
Chromosome Location	chr5:111563955-111563956
allele	A/G
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	TCF12	chr5:111563910-111564957	A549	lung:	n/a	chr5:111564560-111564570
2	EP300	chr5:111563949-111564786	T-47D	breast:	n/a	n/a
3	NFIC	chr5:111563853-111565061	ECC-1	luminal epithelium:	n/a	n/a
4	GATA3	chr5:111563698-111564810	T-47D	breast:	n/a	chr5:111564174-111564181 chr5:111564174-111564181 chr5:111564170-111564186 chr5:111564174-111564181
5	TEAD4	chr5:111563938-111564920	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr5:111563650-111564939	T-47D	breast:	n/a	n/a
7	GATA3	chr5:111563562-111564832	T-47D	breast:	n/a	chr5:111564174-111564181 chr5:111564174-111564181 chr5:111564170-111564186 chr5:111564174-111564181
8	EP300	chr5:111563929-111564923	A549	lung:	n/a	n/a
9	SP1	chr5:111563905-111564932	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111562024..111564609-chr5:133861458..133863356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251076	TF binding region
ENSG00000043143	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10478074	0.89[ASN][1000 genomes]
rs10478076	0.85[ASN][1000 genomes]
rs12652766	0.85[ASN][1000 genomes]
rs12655450	0.94[ASN][1000 genomes]
rs12656841	0.84[ASN][1000 genomes]
rs12719140	0.89[ASN][1000 genomes]
rs13180416	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13184442	0.85[AMR][1000 genomes]
rs13358904	0.89[ASN][1000 genomes]
rs28620667	0.93[ASN][1000 genomes]
rs34489497	0.85[AMR][1000 genomes]
rs34720152	0.86[AMR][1000 genomes]
rs34819608	0.92[ASN][1000 genomes]
rs34947473	0.85[AMR][1000 genomes]
rs35212577	0.85[AMR][1000 genomes]
rs35368594	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35625614	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35776010	0.85[AFR][1000 genomes]
rs35938930	0.85[AMR][1000 genomes]
rs36049225	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4323272	0.84[ASN][1000 genomes]
rs4485968	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4635975	0.90[ASN][1000 genomes]
rs4957637	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4957638	0.86[AMR][1000 genomes]
rs4958023	0.85[AMR][1000 genomes]
rs4958024	0.93[ASN][1000 genomes]
rs4958026	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4958029	0.87[ASN][1000 genomes]
rs56318754	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57970031	0.94[ASN][1000 genomes]
rs59775924	0.94[ASN][1000 genomes]
rs60823180	0.92[ASN][1000 genomes]
rs61475230	0.87[ASN][1000 genomes]
rs61535569	0.92[ASN][1000 genomes]
rs62364080	0.90[ASN][1000 genomes]
rs62364135	0.85[AMR][1000 genomes]
rs62364136	0.85[AMR][1000 genomes]
rs62364145	0.85[AMR][1000 genomes]
rs62370377	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6865000	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6873051	0.86[AMR][1000 genomes]
rs6879361	0.93[ASN][1000 genomes]
rs7715255	0.90[ASN][1000 genomes]
rs7716479	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111504800-111586400	Weak transcription	Gastric	stomach
2	chr5:111554200-111568400	Weak transcription	Right Atrium	heart
3	chr5:111558600-111584400	Weak transcription	Psoas Muscle	Psoas
4	chr5:111558800-111591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:111559400-111564200	Weak transcription	Liver	Liver
6	chr5:111561400-111564200	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:111561400-111564400	Weak transcription	Spleen	Spleen
8	chr5:111562000-111564000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:111562000-111564000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:111562000-111564200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:111562200-111565200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:111562200-111566200	Weak transcription	Fetal Brain Male	brain
13	chr5:111562200-111570200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:111562200-111574400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:111562400-111564200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:111562400-111564400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:111562400-111567800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:111562400-111570200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:111562400-111570800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:111562800-111564800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr5:111562800-111564800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:111562800-111565000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:111562800-111565000	Enhancers	HMEC	breast
24	chr5:111562800-111565200	Enhancers	NHEK	skin
25	chr5:111562800-111572000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:111562800-111573000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:111563000-111565000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:111563200-111564600	Enhancers	Esophagus	oesophagus
29	chr5:111563400-111564000	Weak transcription	Pancreas	Pancrea
30	chr5:111563400-111564800	Enhancers	Fetal Lung	lung
31	chr5:111563400-111564800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr5:111563400-111564800	Flanking Active TSS	A549	lung
33	chr5:111563600-111564000	Weak transcription	Aorta	Aorta
34	chr5:111563600-111564200	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr5:111563600-111564400	Flanking Active TSS	Fetal Heart	heart
36	chr5:111563600-111564600	Enhancers	Placenta	Placenta
37	chr5:111563600-111564600	Enhancers	Left Ventricle	heart
38	chr5:111563600-111564600	Enhancers	Lung	lung
39	chr5:111563600-111564600	Flanking Active TSS	Hela-S3	cervix
40	chr5:111563600-111564800	Enhancers	Stomach Mucosa	stomach
41	chr5:111563800-111564800	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links