Variant report

Variant	rs11754263
Chromosome Location	chr6:110034255-110034256
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	chr6:110034250-110034630	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
FIG4	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10872052	0.81[CEU][hapmap]
rs1096136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096138	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153200	0.80[CEU][hapmap]
rs11751112	0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11753828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11757485	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11759958	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12200787	0.88[EUR][1000 genomes]
rs12524352	0.82[CEU][hapmap]
rs1321327	0.81[CEU][hapmap]
rs1570013	0.81[CEU][hapmap]
rs17540056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17612758	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17612996	0.81[CEU][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1925921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016207	0.81[CEU][hapmap]
rs2064822	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357127	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4523125	0.81[CEU][hapmap]
rs4946982	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946995	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946997	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946998	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947004	1.00[CEU][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56009458	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56125306	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56264193	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58068940	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61170920	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62437563	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62437568	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6568579	0.83[EUR][1000 genomes]
rs6568582	0.83[EUR][1000 genomes]
rs6568583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568595	0.81[CEU][hapmap]
rs6568601	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6568604	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6900133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911851	0.82[EUR][1000 genomes]
rs6912368	0.82[EUR][1000 genomes]
rs6916239	0.84[CEU][hapmap]
rs6917300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924269	0.81[CEU][hapmap]
rs6924436	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6925886	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.88[EUR][1000 genomes]
rs6938741	0.83[EUR][1000 genomes]
rs6942171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7453835	0.81[CEU][hapmap]
rs7756284	0.84[CEU][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7761008	0.81[CEU][hapmap]
rs7772109	0.83[EUR][1000 genomes]
rs7772938	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7775420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829817	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320290	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320300	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320303	1.00[CEU][hapmap]
rs9320304	0.81[CEU][hapmap]
rs9372220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372221	0.81[CEU][hapmap]
rs9372222	0.81[CEU][hapmap]
rs9374095	0.81[CEU][hapmap]
rs9374096	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374108	0.81[CEU][hapmap]
rs9374114	0.80[CEU][hapmap]
rs9386814	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400300	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400312	0.81[CEU][hapmap]
rs9480973	0.81[CEU][hapmap]
rs9487171	0.81[CEU][hapmap]
rs9487175	0.81[CEU][hapmap]
rs9487180	0.81[CEU][hapmap]
rs971432	0.81[CEU][hapmap]
rs9968792	0.87[AMR][1000 genomes];0.89[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
rs11754263	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
2	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
3	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
5	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:110014000-110034400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:110024200-110038800	Weak transcription	Thymus	Thymus
10	chr6:110024200-110056400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:110025000-110034400	Weak transcription	Lung	lung
12	chr6:110025000-110057000	Weak transcription	Fetal Thymus	thymus
13	chr6:110027000-110038200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:110027000-110040400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:110027000-110052400	Weak transcription	Liver	Liver
16	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:110027600-110038600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:110027800-110038200	Weak transcription	Placenta	Placenta
19	chr6:110028000-110036800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:110028000-110038000	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:110028000-110044000	Weak transcription	Brain Angular Gyrus	brain
22	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:110028200-110034400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:110028200-110034600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:110028200-110034600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:110028200-110036200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:110028200-110036200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:110028200-110036800	Weak transcription	Adipose Nuclei	Adipose
29	chr6:110028200-110037600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:110028200-110057200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:110028400-110035000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:110029000-110036600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:110030000-110035400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr6:110032000-110034800	Strong transcription	Primary B cells from cord blood	blood
36	chr6:110033200-110034800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:110033200-110041000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:110034200-110034400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:110034200-110034400	Enhancers	Brain Substantia Nigra	brain
40	chr6:110034200-110034400	Enhancers	NHLF	lung
41	chr6:110034200-110034600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr6:110034200-110034800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:110034200-110034800	Enhancers	Brain Hippocampus Middle	brain
44	chr6:110034200-110034800	Strong transcription	Fetal Intestine Small	intestine
45	chr6:110034200-110035000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:110034200-110035000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:110034200-110035000	Enhancers	HMEC	breast
48	chr6:110034200-110035200	Enhancers	Esophagus	oesophagus
49	chr6:110034200-110035200	Genic enhancers	Spleen	Spleen
50	chr6:110034200-110035400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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