Variant report

Variant	rs34873840
Chromosome Location	chr6:71225724-71225725
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1075262	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10945236	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1208476	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208477	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12190556	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12198920	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12205103	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12215765	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12529284	0.81[ASN][1000 genomes]
rs13202450	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13206086	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13437371	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13654	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16869370	0.82[AFR][1000 genomes]
rs1775338	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1917344	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2347427	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2691505	0.83[EUR][1000 genomes]
rs2691506	0.81[ASN][1000 genomes]
rs2747703	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28360504	0.86[ASN][1000 genomes]
rs34378057	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34710086	0.83[ASN][1000 genomes]
rs35516318	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35542509	0.91[ASN][1000 genomes]
rs3763251	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57836066	0.83[ASN][1000 genomes]
rs62421394	0.86[ASN][1000 genomes]
rs6455371	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906592	0.84[AFR][1000 genomes]
rs6919794	0.83[AFR][1000 genomes]
rs6925112	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6925839	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7341224	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7739098	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7756652	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7769582	0.81[AFR][1000 genomes]
rs7773794	0.87[AFR][1000 genomes]
rs9294874	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9446258	0.86[AFR][1000 genomes]
rs9446274	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9446275	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9455130	0.82[AFR][1000 genomes]
rs9455132	0.86[AFR][1000 genomes]
rs9455133	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9455144	0.86[AFR][1000 genomes]
rs9455179	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9455180	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9455185	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9455186	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs998986	0.81[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	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
6	nsv886145	chr6:71119524-71317480	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv886146	chr6:71219464-71317480	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34873840	C6orf57	cis	Thyroid	GTEx
rs34873840	C6orf57	cis	lung	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71210600-71262000	Weak transcription	Fetal Thymus	thymus
2	chr6:71214000-71236600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:71214000-71244800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:71214000-71248600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:71214000-71248800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:71214000-71249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:71214000-71250600	Weak transcription	Right Ventricle	heart
8	chr6:71214000-71253000	Weak transcription	Colonic Mucosa	Colon
9	chr6:71214000-71253000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:71214000-71256600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:71214000-71276000	Weak transcription	Brain Angular Gyrus	brain
12	chr6:71214000-71276000	Weak transcription	Brain Germinal Matrix	brain
13	chr6:71214000-71276000	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:71214200-71225800	Weak transcription	Ovary	ovary
15	chr6:71214200-71234000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:71214200-71234400	Weak transcription	Liver	Liver
17	chr6:71214200-71248200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:71214400-71226200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:71214400-71226200	Weak transcription	Fetal Brain Male	brain
20	chr6:71214400-71234200	Weak transcription	HepG2	liver
21	chr6:71214400-71238200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:71214400-71246000	Weak transcription	HMEC	breast
23	chr6:71214400-71251000	Weak transcription	Brain Substantia Nigra	brain
24	chr6:71214400-71251800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:71214400-71257000	Weak transcription	Brain Anterior Caudate	brain
26	chr6:71214400-71262000	Weak transcription	Psoas Muscle	Psoas
27	chr6:71214600-71227800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:71214600-71234600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:71214600-71241600	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:71214600-71244000	Weak transcription	Esophagus	oesophagus
31	chr6:71214600-71244400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:71214600-71248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:71214600-71248600	Weak transcription	NHEK	skin
34	chr6:71214600-71248800	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:71214600-71251200	Weak transcription	K562	blood
36	chr6:71214600-71276000	Weak transcription	A549	lung
37	chr6:71214800-71240400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:71215000-71226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:71215000-71273000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:71215200-71234600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:71216000-71232400	Weak transcription	Placenta	Placenta
42	chr6:71216000-71240400	Weak transcription	GM12878-XiMat	blood
43	chr6:71216200-71233400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:71216200-71233600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:71216200-71262200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:71216400-71234400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:71216800-71234800	Weak transcription	Fetal Lung	lung
48	chr6:71218000-71234400	Weak transcription	Left Ventricle	heart
49	chr6:71218000-71234600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr6:71218000-71238600	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links