Variant report

Variant	rs6938689
Chromosome Location	chr6:27437217-27437218
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27410926..27413386-chr6:27436800..27439275,2	K562	blood:
2	chr6:27096577..27099024-chr6:27436212..27439059,2	K562	blood:
3	chr6:27426149..27428000-chr6:27437055..27440025,2	K562	blood:
4	chr6:27434557..27436351-chr6:27436388..27438745,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1014227	0.81[EUR][1000 genomes]
rs10452601	0.81[EUR][1000 genomes]
rs10807025	0.81[AMR][1000 genomes]
rs10946921	0.81[AMR][1000 genomes]
rs10946931	0.81[EUR][1000 genomes]
rs11970336	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12213598	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12215117	0.81[EUR][1000 genomes]
rs13201443	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13201965	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13220155	0.81[EUR][1000 genomes]
rs2049944	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2049945	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2092120	0.82[AMR][1000 genomes]
rs2103557	0.85[AMR][1000 genomes]
rs2142705	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2179154	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2272814	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2272815	0.81[EUR][1000 genomes]
rs2272816	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2893917	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4711153	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4713104	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62401365	0.81[EUR][1000 genomes]
rs6650992	0.81[EUR][1000 genomes]
rs6918794	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6920010	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6920408	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6920733	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6921071	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6933354	0.81[EUR][1000 genomes]
rs7741031	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7745380	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7750795	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7764070	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7771590	0.81[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
3	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv883508	chr6:27434220-27455625	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6938689	ZNF391	cis	Artery Tibial	GTEx
rs6938689	ZNF391	cis	Nerve Tibial	GTEx
rs6938689	ZNF391	cis	lung	GTEx
rs6938689	ZNF391	cis	Heart Left Ventricle	GTEx
rs6938689	ZNF391	cis	Esophagus Muscularis	GTEx
rs6938689	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27412600-27438000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:27415400-27438600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:27424000-27439800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:27425000-27438800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:27425400-27438400	Weak transcription	Fetal Brain Male	brain
6	chr6:27425600-27439400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:27426400-27438200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr6:27426600-27438200	Strong transcription	Fetal Thymus	thymus
9	chr6:27427800-27440000	Weak transcription	Esophagus	oesophagus
10	chr6:27428400-27438800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:27428800-27437800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:27428800-27439800	Weak transcription	Pancreas	Pancrea
13	chr6:27429200-27437400	Weak transcription	Small Intestine	intestine
14	chr6:27429400-27439000	Weak transcription	Stomach Mucosa	stomach
15	chr6:27429600-27437800	Weak transcription	Fetal Heart	heart
16	chr6:27429600-27439800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:27429600-27440000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:27429600-27440000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:27429800-27439000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:27429800-27439800	Weak transcription	Colonic Mucosa	Colon
21	chr6:27430000-27438400	Weak transcription	HepG2	liver
22	chr6:27430000-27438800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:27431200-27437600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:27431200-27437800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr6:27431200-27438000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:27431400-27439400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:27431800-27438800	Strong transcription	HSMM	muscle
28	chr6:27432800-27438800	Weak transcription	NHLF	lung
29	chr6:27433200-27438400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:27433400-27437600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:27433400-27437800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:27433400-27437800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:27433400-27438000	Strong transcription	Primary T cells from cord blood	blood
34	chr6:27433400-27438000	ZNF genes & repeats	GM12878-XiMat	blood
35	chr6:27433400-27438200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr6:27433400-27438200	Strong transcription	Fetal Muscle Leg	muscle
37	chr6:27433400-27438200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:27433400-27439000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr6:27433400-27439400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:27433600-27438000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr6:27433600-27438400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr6:27434000-27437400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:27434000-27438000	Strong transcription	Liver	Liver
44	chr6:27434800-27438800	Weak transcription	NH-A	brain
45	chr6:27435200-27438800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:27435400-27439000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr6:27435400-27439200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:27435400-27439200	Transcr. at gene 5' and 3'	Dnd41	blood
49	chr6:27435400-27440000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:27435600-27437400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links