Variant report

Variant	rs298629
Chromosome Location	chr5:60453162-60453163
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	chr5:60453049-60453422	K562	blood:	n/a	n/a
2	POLR2A	chr5:60452726-60453512	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:60453140-60453291	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:60451693-60455540	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60450120..60453584-chr5:60455423..60459976,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251279	TF binding region
ENSG00000188725	Chromatin interaction
ENSG00000251279	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10939882	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951076	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957772	0.87[EUR][1000 genomes]
rs124898	0.86[EUR][1000 genomes]
rs12518865	0.87[EUR][1000 genomes]
rs12653132	0.83[AFR][1000 genomes]
rs13168191	0.87[EUR][1000 genomes]
rs13171576	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382914	0.81[EUR][1000 genomes]
rs158564	0.83[EUR][1000 genomes]
rs158923	0.81[EUR][1000 genomes]
rs158924	0.81[EUR][1000 genomes]
rs159358	0.86[EUR][1000 genomes]
rs159376	0.84[EUR][1000 genomes]
rs159377	0.86[EUR][1000 genomes]
rs159378	0.86[EUR][1000 genomes]
rs159380	0.86[EUR][1000 genomes]
rs159537	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162234	0.83[EUR][1000 genomes]
rs162238	0.82[EUR][1000 genomes]
rs162241	0.81[EUR][1000 genomes]
rs162242	0.82[EUR][1000 genomes]
rs162244	0.81[EUR][1000 genomes]
rs162247	0.81[EUR][1000 genomes]
rs172348	0.81[EUR][1000 genomes]
rs172945	0.82[EUR][1000 genomes]
rs182410	0.86[EUR][1000 genomes]
rs185354	0.81[EUR][1000 genomes]
rs187459	0.85[EUR][1000 genomes]
rs2080869	0.87[EUR][1000 genomes]
rs2112365	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263514	0.81[EUR][1000 genomes]
rs248677	0.82[EUR][1000 genomes]
rs248682	0.87[EUR][1000 genomes]
rs248685	0.87[EUR][1000 genomes]
rs2545475	0.87[EUR][1000 genomes]
rs2545478	0.87[EUR][1000 genomes]
rs2545503	0.88[EUR][1000 genomes]
rs2650512	0.81[EUR][1000 genomes]
rs2650517	0.81[EUR][1000 genomes]
rs2694530	0.81[EUR][1000 genomes]
rs2694531	0.81[EUR][1000 genomes]
rs290503	0.82[EUR][1000 genomes]
rs290506	0.82[EUR][1000 genomes]
rs290507	0.82[EUR][1000 genomes]
rs2950235	0.81[EUR][1000 genomes]
rs295522	0.86[EUR][1000 genomes]
rs295532	0.84[EUR][1000 genomes]
rs295533	0.87[EUR][1000 genomes]
rs295551	0.87[EUR][1000 genomes]
rs295560	0.86[EUR][1000 genomes]
rs295566	0.87[EUR][1000 genomes]
rs295569	0.86[EUR][1000 genomes]
rs295579	0.86[EUR][1000 genomes]
rs3108388	0.81[EUR][1000 genomes]
rs329622	0.82[EUR][1000 genomes]
rs329623	0.82[EUR][1000 genomes]
rs329625	0.82[EUR][1000 genomes]
rs329626	0.80[EUR][1000 genomes]
rs34593	0.82[EUR][1000 genomes]
rs34609	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34613	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34614	0.86[EUR][1000 genomes]
rs34616	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34617	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34621	0.86[EUR][1000 genomes]
rs34624	0.87[EUR][1000 genomes]
rs34625	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34636	0.86[EUR][1000 genomes]
rs34637	0.86[EUR][1000 genomes]
rs34639	0.85[EUR][1000 genomes]
rs34644	0.85[EUR][1000 genomes]
rs39661	0.86[EUR][1000 genomes]
rs40084	0.85[EUR][1000 genomes]
rs4141502	0.87[EUR][1000 genomes]
rs4699969	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159106	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56284222	0.81[AFR][1000 genomes]
rs56409036	0.82[EUR][1000 genomes]
rs6878124	0.87[EUR][1000 genomes]
rs6886481	0.87[EUR][1000 genomes]
rs723276	0.87[EUR][1000 genomes]
rs7701839	0.86[EUR][1000 genomes]
rs7706753	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721096	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs810883	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598314	chr5:60374912-60459040	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS 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	31 gene(s)	inside rSNPs	diseases
4	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs298629	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60398800-60453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60436000-60457600	Weak transcription	Esophagus	oesophagus
3	chr5:60438000-60455400	Weak transcription	Fetal Brain Female	brain
4	chr5:60438600-60455600	Weak transcription	Fetal Kidney	kidney
5	chr5:60438800-60455800	Weak transcription	Brain Germinal Matrix	brain
6	chr5:60440400-60457400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:60440600-60455800	Weak transcription	Left Ventricle	heart
8	chr5:60441000-60455800	Weak transcription	Pancreas	Pancrea
9	chr5:60442400-60455800	Weak transcription	NHLF	lung
10	chr5:60445400-60455000	Weak transcription	Fetal Lung	lung
11	chr5:60445600-60455600	Weak transcription	Primary T cells from cord blood	blood
12	chr5:60446200-60454600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:60446600-60457400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:60446800-60456600	Weak transcription	Fetal Stomach	stomach
15	chr5:60447400-60457400	Weak transcription	Ovary	ovary
16	chr5:60448200-60453600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:60448200-60453800	Weak transcription	NH-A	brain
18	chr5:60448200-60454200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:60449000-60457200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:60449200-60455400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:60449600-60454200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:60449800-60454400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:60450000-60455000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:60450000-60457400	Weak transcription	Right Ventricle	heart
25	chr5:60450200-60455000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:60450200-60455600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:60450400-60457600	Weak transcription	Lung	lung
28	chr5:60450600-60454000	Weak transcription	Osteobl	bone
29	chr5:60450600-60455600	Weak transcription	Fetal Intestine Large	intestine
30	chr5:60450800-60456400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:60451000-60453600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:60451000-60455000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:60451000-60455800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:60451000-60457200	Weak transcription	Thymus	Thymus
35	chr5:60451200-60453400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:60451200-60455800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:60451200-60456600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:60451400-60453800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:60451400-60454600	Weak transcription	Hela-S3	cervix
40	chr5:60451400-60457000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:60451600-60453800	Weak transcription	HepG2	liver
42	chr5:60451600-60454000	Weak transcription	HMEC	breast
43	chr5:60451600-60455800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:60451600-60456400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr5:60451800-60454600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:60451800-60457600	Weak transcription	Spleen	Spleen
47	chr5:60452000-60453400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr5:60452000-60453400	ZNF genes & repeats	Fetal Thymus	thymus
49	chr5:60452000-60453600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:60452000-60454600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links