Variant report

Variant	rs13085679
Chromosome Location	chr3:49869631-49869632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49868258..49870726-chr3:49875170..49876844,2	MCF-7	breast:
2	chr3:49868893..49870758-chr3:49882070..49883892,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10049413	0.95[ASN][1000 genomes]
rs1049256	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10865958	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865959	0.95[ASN][1000 genomes]
rs11130214	0.85[ASN][1000 genomes]
rs11130216	0.85[ASN][1000 genomes]
rs11130218	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130219	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130221	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1128535	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709680	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11710675	0.87[ASN][1000 genomes]
rs11714957	0.89[ASN][1000 genomes]
rs11715304	0.98[ASN][1000 genomes]
rs11716575	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11717256	0.99[ASN][1000 genomes]
rs11717463	0.89[ASN][1000 genomes]
rs11920900	0.88[ASN][1000 genomes]
rs12381242	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12490656	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13063621	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13084243	0.89[ASN][1000 genomes]
rs13086130	0.89[ASN][1000 genomes]
rs13086465	0.87[ASN][1000 genomes]
rs13090611	0.83[ASN][1000 genomes]
rs1317140	0.89[ASN][1000 genomes]
rs13316065	0.94[ASN][1000 genomes]
rs1491986	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1799843	0.96[ASN][1000 genomes]
rs1799845	0.96[ASN][1000 genomes]
rs2234385	0.96[ASN][1000 genomes]
rs2234391	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246832	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247036	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271960	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271961	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276864	0.95[ASN][1000 genomes]
rs2291542	0.87[ASN][1000 genomes]
rs2307021	0.87[ASN][1000 genomes]
rs2352967	0.94[ASN][1000 genomes]
rs2352974	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2352975	0.95[ASN][1000 genomes]
rs34451146	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34522271	0.89[ASN][1000 genomes]
rs34614773	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34735338	0.89[ASN][1000 genomes]
rs35210174	0.89[ASN][1000 genomes]
rs35261599	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35474403	0.89[ASN][1000 genomes]
rs3749237	0.89[ASN][1000 genomes]
rs3749240	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3749241	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3811695	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3811696	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3819325	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4519692	0.89[ASN][1000 genomes]
rs4768	0.87[ASN][1000 genomes]
rs4855841	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855850	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855862	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855867	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57648519	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59906301	0.84[ASN][1000 genomes]
rs60205400	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260715	0.89[ASN][1000 genomes]
rs62260719	0.96[ASN][1000 genomes]
rs62260729	0.95[ASN][1000 genomes]
rs6446295	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6766836	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775384	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785549	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6802890	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6804655	0.85[ASN][1000 genomes]
rs695238	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324996	0.84[ASN][1000 genomes]
rs7372725	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372730	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7372966	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7374183	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7374277	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7426497	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7429353	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431078	0.89[ASN][1000 genomes]
rs7431106	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7618501	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7618519	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7629936	0.93[ASN][1000 genomes]
rs7634886	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7634902	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7645061	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648987	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649348	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9814765	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9815766	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9819511	0.93[ASN][1000 genomes]
rs9850465	0.93[ASN][1000 genomes]
rs9853458	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9855505	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859153	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9865480	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871654	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9872864	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873183	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9876508	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9882639	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv967270	chr3:49845381-49870409	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13085679	RBM6	cis	Artery Tibial	GTEx
rs13085679	RBM6	cis	lung	GTEx
rs13085679	FAM212A	cis	Esophagus Mucosa	GTEx
rs13085679	RBM6	cis	Esophagus Muscularis	GTEx
rs13085679	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs13085679	RBM6	cis	Nerve Tibial	GTEx
rs13085679	RBM6	cis	Whole Blood	GTEx
rs13085679	RBM6	cis	Thyroid	GTEx
rs13085679	UBA7	cis	Whole Blood	GTEx
rs13085679	UBA7	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49882200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49863400-49876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:49863400-49876800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:49863400-49879000	Weak transcription	Fetal Brain Male	brain
6	chr3:49863600-49876600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:49863800-49874000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:49863800-49875600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:49863800-49879000	Weak transcription	NH-A	brain
10	chr3:49863800-49882800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:49864000-49876600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:49864000-49883200	Weak transcription	Colonic Mucosa	Colon
13	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
14	chr3:49864200-49873000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:49864200-49876800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:49864400-49876800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:49864600-49876800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:49864600-49882000	Weak transcription	Osteobl	bone
20	chr3:49864800-49872800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:49864800-49878000	Strong transcription	Fetal Thymus	thymus
22	chr3:49864800-49880400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:49865000-49869800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:49865000-49870800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:49865000-49872400	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:49865000-49872800	Strong transcription	Fetal Stomach	stomach
28	chr3:49865000-49876400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49865000-49876400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:49865000-49886000	Strong transcription	Dnd41	blood
31	chr3:49865200-49872000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:49865200-49872200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:49865200-49872400	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr3:49865200-49872800	Strong transcription	Fetal Intestine Small	intestine
35	chr3:49865200-49876200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:49865200-49877000	Weak transcription	Right Ventricle	heart
37	chr3:49865200-49877400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:49865400-49870000	Weak transcription	HSMM	muscle
39	chr3:49865600-49869800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:49865600-49876000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:49865600-49876800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:49865800-49869800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:49865800-49869800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:49865800-49869800	Strong transcription	Fetal Intestine Large	intestine
47	chr3:49866000-49881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:49866200-49870000	Strong transcription	HepG2	liver
49	chr3:49866200-49871800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:49866200-49872200	Strong transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links