Variant report

Variant	rs35460909
Chromosome Location	chr5:178050709-178050710
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	chr5:178050622-178051223	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:178029668..178031491-chr5:178050533..178053383,2	K562	blood:
2	chr5:178035433..178037862-chr5:178050507..178052447,2	K562	blood:
3	chr5:178049762..178051706-chr5:178156637..178158195,2	MCF-7	breast:

Variant related genes	Relation type
RN7SKP70	TF binding region
CLK4	TF binding region
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11249553	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249554	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11737903	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740194	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11746942	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11747742	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12514311	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12518589	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13155255	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13156622	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35522922	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36008351	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs501721	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs519984	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs530542	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs574103	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs576097	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs584415	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs596780	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs602019	0.96[ASN][1000 genomes]
rs602451	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628857	0.84[AMR][1000 genomes]
rs643936	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs649585	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6882079	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6886390	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs721144	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7702727	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7732660	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35460909	CLK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178026400-178050800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:178031800-178052800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:178035800-178052000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:178037800-178050800	Weak transcription	Stomach Mucosa	stomach
5	chr5:178041600-178051200	Weak transcription	Right Ventricle	heart
6	chr5:178042200-178051400	Weak transcription	Pancreas	Pancrea
7	chr5:178043400-178051400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:178044000-178051400	Weak transcription	Fetal Intestine Small	intestine
9	chr5:178044000-178052000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:178044000-178052000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:178044600-178051000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:178047000-178051200	Weak transcription	Aorta	Aorta
13	chr5:178047000-178051600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:178047000-178052000	Weak transcription	Esophagus	oesophagus
15	chr5:178047000-178052200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:178047200-178050800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr5:178047200-178051000	Weak transcription	Psoas Muscle	Psoas
18	chr5:178047200-178051200	Weak transcription	Fetal Stomach	stomach
19	chr5:178047200-178051400	Weak transcription	Gastric	stomach
20	chr5:178047200-178052000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:178047400-178051400	Weak transcription	Spleen	Spleen
22	chr5:178047400-178052000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:178047400-178052000	Weak transcription	Lung	lung
24	chr5:178047600-178051800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:178047800-178051200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:178048200-178050800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:178048200-178051200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:178048200-178051800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:178048400-178051200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:178048400-178051200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr5:178048400-178051600	Weak transcription	Colonic Mucosa	Colon
32	chr5:178048800-178051000	Weak transcription	HSMMtube	muscle
33	chr5:178049600-178051000	Weak transcription	Fetal Brain Male	brain
34	chr5:178049600-178051200	Weak transcription	Thymus	Thymus
35	chr5:178049800-178051000	Weak transcription	HUVEC	blood vessel
36	chr5:178049800-178051400	Enhancers	Fetal Heart	heart
37	chr5:178050000-178050800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:178050000-178051000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr5:178050000-178051000	Weak transcription	NHLF	lung
40	chr5:178050000-178051200	Enhancers	Colon Smooth Muscle	Colon
41	chr5:178050000-178051200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr5:178050000-178051400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr5:178050000-178051400	Enhancers	Brain Angular Gyrus	brain
44	chr5:178050000-178051400	Enhancers	Brain Anterior Caudate	brain
45	chr5:178050000-178051400	Enhancers	Brain Germinal Matrix	brain
46	chr5:178050200-178050800	Enhancers	Small Intestine	intestine
47	chr5:178050200-178051000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:178050200-178051000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:178050200-178051000	Weak transcription	Fetal Lung	lung
50	chr5:178050200-178051000	Weak transcription	Hela-S3	cervix

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