Variant report

Variant	rs56125306
Chromosome Location	chr6:110024466-110024467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1096136	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1096138	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11751112	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11753828	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11754263	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11757485	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11759958	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12200787	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17540056	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17612758	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17612996	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1885425	0.82[EUR][1000 genomes]
rs1925921	0.86[EUR][1000 genomes]
rs2064822	0.87[EUR][1000 genomes]
rs2145144	0.81[EUR][1000 genomes]
rs2357127	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4296926	0.85[EUR][1000 genomes]
rs4946982	0.86[EUR][1000 genomes]
rs4946995	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4946997	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4946998	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4947004	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4947006	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56009458	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56264193	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58068940	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61170920	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62437563	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62437568	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6568579	0.86[EUR][1000 genomes]
rs6568582	0.85[EUR][1000 genomes]
rs6568583	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6568591	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6568596	0.82[EUR][1000 genomes]
rs6568601	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6568604	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6900133	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6900187	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6911851	0.85[EUR][1000 genomes]
rs6912368	0.85[EUR][1000 genomes]
rs6917300	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6918140	0.82[EUR][1000 genomes]
rs6921303	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6924269	0.82[EUR][1000 genomes]
rs6924436	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6925886	0.86[EUR][1000 genomes]
rs6931630	0.90[EUR][1000 genomes]
rs6932774	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6938741	0.86[EUR][1000 genomes]
rs6942171	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7756284	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7771729	0.84[EUR][1000 genomes]
rs7772109	0.86[EUR][1000 genomes]
rs7772938	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7773915	0.82[EUR][1000 genomes]
rs7775420	0.87[EUR][1000 genomes]
rs829817	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs911022	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs911023	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9320290	0.86[EUR][1000 genomes]
rs9320300	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9372220	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9374096	0.87[EUR][1000 genomes]
rs9386814	0.87[EUR][1000 genomes]
rs9400289	0.86[EUR][1000 genomes]
rs9400300	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9968792	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56125306	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110024800	Weak transcription	Lung	lung
2	chr6:110013000-110025200	Weak transcription	Small Intestine	intestine
3	chr6:110013000-110027400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:110013000-110027400	Weak transcription	Spleen	Spleen
5	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
6	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
7	chr6:110013200-110026400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:110013200-110026600	Weak transcription	Ovary	ovary
9	chr6:110013200-110034000	Weak transcription	Fetal Stomach	stomach
10	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
12	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:110013800-110026400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:110013800-110026600	Weak transcription	Brain Substantia Nigra	brain
17	chr6:110013800-110029600	Weak transcription	Fetal Lung	lung
18	chr6:110014000-110027400	Weak transcription	Brain Angular Gyrus	brain
19	chr6:110014000-110034400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:110014600-110026600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:110014800-110026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:110014800-110026400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:110014800-110026600	Weak transcription	Liver	Liver
24	chr6:110014800-110026800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:110014800-110027400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:110014800-110027400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:110014800-110034200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:110015000-110026200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:110015000-110026200	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:110017600-110027000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:110018000-110024800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:110018200-110026600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:110018800-110034200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:110019000-110026600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:110020600-110027800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr6:110022200-110025000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:110022200-110025200	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr6:110022200-110025200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:110022200-110028200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:110022400-110024600	Enhancers	Adipose Nuclei	Adipose
41	chr6:110022600-110024600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:110022600-110024600	Enhancers	Primary B cells from cord blood	blood
43	chr6:110022600-110026600	Weak transcription	Brain Anterior Caudate	brain
44	chr6:110022600-110029400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:110022800-110027600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:110023200-110024600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:110023200-110025000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:110023200-110026600	Weak transcription	Psoas Muscle	Psoas
49	chr6:110023200-110026800	Weak transcription	GM12878-XiMat	blood
50	chr6:110023400-110025200	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links