Variant report

Variant	rs2758848
Chromosome Location	chr6:86347605-86347606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86338900..86342073-chr6:86344081..86348707,4	MCF-7	breast:
2	chr6:86338689..86357756-chr6:86378394..86390434,115	MCF-7	breast:
3	chr6:86326511..86329111-chr6:86347081..86350058,3	K562	blood:
4	chr6:86327554..86329111-chr6:86347081..86350058,2	K562	blood:
5	chr6:86342168..86343867-chr6:86346506..86348145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236016	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1059306	0.83[CEU][hapmap]
rs1059307	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10944128	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs10944129	0.83[EUR][1000 genomes]
rs1173416	0.81[EUR][1000 genomes]
rs1173417	0.83[CEU][hapmap]
rs1173418	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11752795	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12193777	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12199873	0.83[CEU][hapmap]
rs12203963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12206573	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12212560	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]
rs2475790	0.83[CEU][hapmap]
rs2475792	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs2758840	0.83[CEU][hapmap]
rs2758842	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]
rs2758843	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2758845	0.91[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap]
rs2758847	0.83[CEU][hapmap]
rs2758849	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783171	0.83[CEU][hapmap]
rs2842600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842601	0.83[CEU][hapmap]
rs2842603	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs2842605	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2842607	0.83[CEU][hapmap]
rs2842608	0.83[CEU][hapmap]
rs2842609	0.83[CEU][hapmap]
rs2842610	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842612	0.82[CEU][hapmap]
rs2842613	0.83[CEU][hapmap]
rs2842614	0.91[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap]
rs2842615	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087978	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34980280	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4296866	0.85[GIH][hapmap]
rs4304137	0.83[CEU][hapmap]
rs4348284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351223	0.83[CEU][hapmap]
rs4431401	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes]
rs4593336	0.84[CHD][hapmap]
rs4640862	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707212	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6454471	0.83[CEU][hapmap]
rs6454472	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6909767	0.91[CEU][hapmap]
rs6922	0.83[CEU][hapmap]
rs6927475	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6935918	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs7452605	0.83[CEU][hapmap]
rs7742201	0.82[CEU][hapmap]
rs7742691	0.95[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]
rs7766485	1.00[ASW][hapmap];0.96[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs7775864	0.87[CHB][hapmap]
rs911927	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs9294337	0.83[CEU][hapmap]
rs9342045	0.92[EUR][1000 genomes]
rs9344533	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap]
rs9344540	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9344542	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs9351065	0.83[CEU][hapmap]
rs9353318	0.83[CEU][hapmap]
rs9353327	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs9362230	0.83[CEU][hapmap]
rs9362232	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444348	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs9444351	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444354	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450282	0.84[CHD][hapmap]
rs9450284	0.82[CEU][hapmap]
rs9450285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450288	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs9450292	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450302	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs9450311	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS 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	124 gene(s)	inside rSNPs	diseases
4	nsv5383	chr6:86303223-86348023	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2758848	SNHG5	cis	Thyroid	GTEx
rs2758848	C6orf160	cis	lesional skin	skin_eQTL
rs2758848	SNHG5	cis	Muscle Skeletal	GTEx
rs2758848	SNHG5	cis	Whole Blood	GTEx
rs2758848	SNORD50B	cis	parietal	SCAN
rs2758848	SNHG5	cis	Nerve Tibial	GTEx
rs2758848	C6orf160	cis	uninvolved skin	skin_eQTL
rs2758848	SNHG5	cis	Artery Tibial	GTEx
rs2758848	SNHG5	cis	Adipose Subcutaneous	GTEx
rs2758848	SNHG5	cis	lung	GTEx
rs2758848	C6orf160	cis	normal skin	skin_eQTL
rs2758848	SNHG5	cis	Artery Aorta	GTEx
rs2758848	SNHG5	cis	lymphoblastoid	seeQTL
rs2758848	SNHG5	cis	Esophagus Muscularis	GTEx
rs2758848	SNHG5	cis	Heart Left Ventricle	GTEx
rs2758848	SNHG5	cis	multi-tissue	Pritchard
rs2758848	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs2758848	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs2758848	SNHG5	cis	Stomach	GTEx
rs2758848	SNHG5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr6:86314800-86348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:86315000-86347800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:86316000-86348600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:86316200-86347800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr6:86316200-86348600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:86316200-86348600	Strong transcription	Placenta	Placenta
8	chr6:86316200-86348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:86316400-86348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:86316400-86348400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:86316400-86349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
13	chr6:86317000-86349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:86317400-86349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr6:86317800-86348200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:86318600-86348800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr6:86319400-86348600	Strong transcription	K562	blood
20	chr6:86319600-86348200	Strong transcription	NHEK	skin
21	chr6:86319600-86348800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:86320000-86348600	Strong transcription	Liver	Liver
24	chr6:86320200-86350400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr6:86321000-86348600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:86321000-86349600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:86323600-86349000	Strong transcription	Fetal Intestine Large	intestine
28	chr6:86323600-86351200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:86324800-86348600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:86326400-86349200	Strong transcription	Primary hematopoietic stem cells	blood
31	chr6:86328000-86349800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:86331400-86348400	Strong transcription	NHDF-Ad	bronchial
33	chr6:86331400-86349000	Strong transcription	HSMM	muscle
34	chr6:86332400-86349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:86335000-86348200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:86335200-86349600	Strong transcription	Fetal Muscle Leg	muscle
37	chr6:86335600-86348200	Strong transcription	Fetal Lung	lung
38	chr6:86335600-86349000	Strong transcription	Adipose Nuclei	Adipose
39	chr6:86335600-86349200	Strong transcription	Fetal Kidney	kidney
40	chr6:86336200-86348200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:86337800-86348000	Strong transcription	Primary T cells from cord blood	blood
42	chr6:86338200-86348600	Strong transcription	Thymus	Thymus
43	chr6:86338600-86348400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:86338800-86349000	Strong transcription	Osteobl	bone
45	chr6:86339000-86349200	Strong transcription	NH-A	brain
46	chr6:86339200-86348200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:86339200-86349200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:86340000-86349400	Strong transcription	Primary B cells from cord blood	blood
49	chr6:86340200-86349000	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr6:86340400-86350400	Weak transcription	Aorta	Aorta

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