Variant report

Variant	rs6858302
Chromosome Location	chr4:152101230-152101231
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	POLR2A	chr4:152101162-152101261	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152100696..152102854-chr4:152105913..152107638,2	MCF-7	breast:

Variant related genes	Relation type
SH3D19	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10009307	0.83[ASN][1000 genomes]
rs12501643	0.82[ASN][1000 genomes]
rs12503016	0.82[ASN][1000 genomes]
rs12508270	0.93[ASN][1000 genomes]
rs12511209	0.83[ASN][1000 genomes]
rs17633530	0.83[ASN][1000 genomes]
rs17633537	0.83[ASN][1000 genomes]
rs28593016	0.83[ASN][1000 genomes]
rs28694456	0.83[ASN][1000 genomes]
rs36115072	0.97[ASN][1000 genomes]
rs3736502	0.83[ASN][1000 genomes]
rs3762846	0.83[ASN][1000 genomes]
rs58496896	0.83[ASN][1000 genomes]
rs60367453	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60953992	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61442068	0.96[ASN][1000 genomes]
rs6535764	0.81[ASN][1000 genomes]
rs7675432	0.81[ASN][1000 genomes]
rs7681468	0.96[ASN][1000 genomes]
rs7681571	0.98[ASN][1000 genomes]
rs7682480	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv595690	chr4:151788955-152109552	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
7	nsv1026416	chr4:151847403-152105879	Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6858302	RPS3A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152055000-152105800	Weak transcription	Small Intestine	intestine
2	chr4:152088000-152101600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:152088200-152114600	Weak transcription	Psoas Muscle	Psoas
4	chr4:152090400-152105800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:152091200-152103800	Weak transcription	Fetal Brain Male	brain
6	chr4:152091200-152107000	Weak transcription	HSMMtube	muscle
7	chr4:152095800-152105600	Weak transcription	Stomach Mucosa	stomach
8	chr4:152096400-152103200	Weak transcription	Esophagus	oesophagus
9	chr4:152096600-152105600	Weak transcription	Gastric	stomach
10	chr4:152096600-152106200	Weak transcription	Right Ventricle	heart
11	chr4:152096600-152106200	Weak transcription	NHEK	skin
12	chr4:152096600-152118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:152096800-152102400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:152096800-152106400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:152096800-152106400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:152096800-152120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:152097000-152105200	Weak transcription	A549	lung
18	chr4:152097200-152103400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:152097200-152106400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:152097200-152123600	Weak transcription	Pancreas	Pancrea
21	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
22	chr4:152097400-152105800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:152097400-152111600	Weak transcription	Lung	lung
24	chr4:152097400-152123600	Weak transcription	Aorta	Aorta
25	chr4:152097600-152102400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:152097600-152110800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:152097600-152111400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:152097600-152111600	Weak transcription	Fetal Stomach	stomach
29	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:152097800-152103600	Weak transcription	Fetal Lung	lung
31	chr4:152097800-152105600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:152097800-152105800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:152097800-152105800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:152097800-152105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:152097800-152105800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:152097800-152106200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:152097800-152110000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:152097800-152111400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:152097800-152117200	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:152097800-152120000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr4:152098000-152105600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:152098000-152105800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:152098000-152105800	Weak transcription	HUVEC	blood vessel
44	chr4:152098000-152107400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:152098200-152105200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:152098200-152105600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:152098200-152105600	Weak transcription	Osteobl	bone
48	chr4:152098200-152106000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:152098200-152106200	Weak transcription	Left Ventricle	heart
50	chr4:152098200-152106200	Weak transcription	Ovary	ovary

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