Variant report

Variant	rs2268993
Chromosome Location	chr6:88184111-88184112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88180469..88184304-chr6:88409511..88413377,7	K562	blood:
2	chr6:88182819..88184854-chr6:88208059..88210362,2	K562	blood:
3	chr6:88109062..88110726-chr6:88183109..88185795,2	MCF-7	breast:
4	chr6:88181828..88184241-chr6:88195546..88199503,4	MCF-7	breast:
5	chr6:88118527..88120089-chr6:88183181..88184775,2	MCF-7	breast:
6	chr6:88180469..88184304-chr6:88409409..88413377,5	K562	blood:

Variant related genes	Relation type
ENSG00000206715	Chromatin interaction
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1051131	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1051148	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10755484	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs13193380	0.82[EUR][1000 genomes]
rs13214153	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs2103764	0.86[ASN][1000 genomes]
rs2207144	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs2207146	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2268994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284908	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300906	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2300909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2325064	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2754245	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs2754247	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs3757368	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3918467	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap]
rs3934838	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs4334949	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs4464759	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs448580	0.81[MEX][hapmap]
rs4587138	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4587143	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs4707373	0.82[EUR][1000 genomes]
rs4707374	0.83[EUR][1000 genomes]
rs4707376	0.81[EUR][1000 genomes]
rs4707377	0.81[EUR][1000 genomes]
rs4707379	0.81[EUR][1000 genomes]
rs6454630	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454631	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6454632	0.86[EUR][1000 genomes]
rs6905947	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs6906769	0.86[EUR][1000 genomes]
rs6912958	0.81[ASN][1000 genomes]
rs6914299	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs6916732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs6918909	0.81[EUR][1000 genomes]
rs6923230	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6928160	0.81[EUR][1000 genomes]
rs6933587	0.95[CHB][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6940150	0.81[EUR][1000 genomes]
rs7741825	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7742965	0.82[EUR][1000 genomes]
rs7750207	0.81[EUR][1000 genomes]
rs7754350	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7757636	0.83[EUR][1000 genomes]
rs7761814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7762864	0.86[EUR][1000 genomes]
rs7773906	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs9294379	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs9294381	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs9444504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9444512	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9444519	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs9444522	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs9444524	0.81[EUR][1000 genomes]
rs9450688	0.86[ASN][1000 genomes]
rs9450701	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450712	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9450732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs9450733	0.85[EUR][1000 genomes]
rs9450738	0.81[EUR][1000 genomes]
rs9450739	0.81[EUR][1000 genomes]
rs9450744	0.81[EUR][1000 genomes]
rs9450752	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs9450755	0.81[EUR][1000 genomes]
rs985764	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2268993	SLC35A1	cis	parietal	SCAN
rs2268993	SLC35A1	cis	multi-tissue	Pritchard
rs2268993	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2268993	SNORD50A	cis	cerebellum	SCAN
rs2268993	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2268993	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2268993	ZNF567	trans	lymphoblastoid	RTeQTL
rs2268993	C6orf162	cis	cerebellum	SCAN
rs2268993	SLC35A1	cis	lymphoblastoid	seeQTL
rs2268993	C6orf162	cis	parietal	SCAN
rs2268993	C6orf164	cis	Thyroid	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88182000-88184200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:88182000-88184400	Active TSS	Right Atrium	heart
3	chr6:88183000-88184200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:88183200-88184200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr6:88183200-88184200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr6:88183200-88184600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr6:88183400-88184400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr6:88183600-88184400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:88183600-88184400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:88183600-88184400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:88183600-88184400	Enhancers	Liver	Liver
12	chr6:88183600-88184400	Enhancers	Brain Substantia Nigra	brain
13	chr6:88183600-88184600	Weak transcription	Stomach Mucosa	stomach
14	chr6:88183600-88185200	Enhancers	Primary T cells from cord blood	blood
15	chr6:88183600-88187400	Weak transcription	Left Ventricle	heart
16	chr6:88183600-88187400	Weak transcription	Ovary	ovary
17	chr6:88183600-88190200	Weak transcription	Spleen	Spleen
18	chr6:88183600-88193000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:88183600-88193200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:88183600-88193200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:88183600-88193200	Weak transcription	Lung	lung
22	chr6:88183600-88193400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:88183600-88193600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:88183600-88212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:88183600-88226000	Weak transcription	Gastric	stomach
26	chr6:88183800-88184200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr6:88183800-88184200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:88183800-88184200	Enhancers	Small Intestine	intestine
29	chr6:88183800-88184200	Enhancers	HSMM	muscle
30	chr6:88183800-88184200	Enhancers	NHEK	skin
31	chr6:88183800-88184400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:88183800-88184400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:88183800-88184400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:88183800-88184400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr6:88183800-88184400	Active TSS	GM12878-XiMat	blood
36	chr6:88183800-88184400	Enhancers	HepG2	liver
37	chr6:88183800-88184400	Enhancers	HUVEC	blood vessel
38	chr6:88183800-88184800	Enhancers	Fetal Lung	lung
39	chr6:88183800-88185200	Enhancers	Dnd41	blood
40	chr6:88183800-88186000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:88183800-88187000	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:88183800-88187200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:88183800-88187200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:88183800-88187200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr6:88183800-88187200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:88183800-88187400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:88183800-88187400	Weak transcription	Fetal Intestine Large	intestine
48	chr6:88183800-88187400	Weak transcription	Fetal Thymus	thymus
49	chr6:88183800-88187400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:88183800-88187800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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