Variant report

Variant	rs6454471
Chromosome Location	chr6:86214456-86214457
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86212509..86214733-chr6:86218733..86220237,2	K562	blood:
2	chr6:86213906..86216612-chr6:86245425..86247790,2	K562	blood:
3	chr6:86207297..86209802-chr6:86213073..86214625,2	K562	blood:

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1059306	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10944133	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1173415	0.81[ASN][1000 genomes]
rs1173417	0.83[CEU][hapmap]
rs12199873	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12203963	0.84[CEU][hapmap]
rs12205013	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12212560	0.87[CEU][hapmap]
rs1885607	0.84[AFR][1000 genomes]
rs2065114	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs2208725	0.81[ASN][1000 genomes]
rs2229523	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2475790	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2475791	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2475792	0.86[CEU][hapmap]
rs2758840	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2758842	0.91[CEU][hapmap]
rs2758843	0.91[CEU][hapmap]
rs2758844	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2758845	0.91[CEU][hapmap]
rs2758846	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2758847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2758848	0.83[CEU][hapmap]
rs2783171	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842600	0.83[CEU][hapmap]
rs2842601	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2842602	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2842603	0.87[CEU][hapmap]
rs2842604	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2842607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2842608	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842609	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842611	0.83[CEU][hapmap]
rs2842612	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2842613	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2842614	0.91[CEU][hapmap]
rs3087978	0.83[CEU][hapmap]
rs3812133	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4235826	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4235827	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4282381	0.82[ASN][1000 genomes]
rs4304137	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4348284	0.84[CEU][hapmap]
rs4351223	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4419647	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4431401	0.83[CEU][hapmap]
rs4441928	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4501401	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4562107	0.81[ASN][1000 genomes]
rs4579322	0.85[CHB][hapmap]
rs4706240	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707207	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4707209	0.92[ASN][1000 genomes]
rs4707211	0.84[CEU][hapmap]
rs6454468	0.82[ASN][1000 genomes]
rs6454469	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6909767	0.91[CEU][hapmap]
rs6922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926049	0.91[ASN][1000 genomes]
rs6931295	0.81[ASN][1000 genomes]
rs6935918	0.91[CEU][hapmap]
rs7452605	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7742691	0.91[CEU][hapmap]
rs7746065	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7768065	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7770359	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap]
rs911927	0.91[CEU][hapmap]
rs9294337	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9344532	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9344533	0.91[CEU][hapmap]
rs9344542	0.87[CEU][hapmap]
rs9351065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9353318	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9353327	0.87[CEU][hapmap]
rs9362230	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9362233	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444349	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9444352	0.83[CEU][hapmap]
rs9450284	0.82[CEU][hapmap]
rs9450285	0.83[CEU][hapmap]
rs9450290	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450302	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv463939	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv470839	chr6:86205323-86279737	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv604093	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6454471	SNHG5	cis	Esophagus Muscularis	GTEx
rs6454471	C6orf160	cis	uninvolved skin	skin_eQTL
rs6454471	SNHG5	cis	Artery Tibial	GTEx
rs6454471	SNHG5	cis	lung	GTEx
rs6454471	C6orf160	cis	normal skin	skin_eQTL
rs6454471	SNHG5	cis	Heart Left Ventricle	GTEx
rs6454471	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs6454471	SNHG5	cis	Muscle Skeletal	GTEx
rs6454471	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs6454471	SNHG5	cis	Adipose Subcutaneous	GTEx
rs6454471	SNHG5	cis	Thyroid	GTEx
rs6454471	SNHG5	cis	multi-tissue	Pritchard
rs6454471	C6orf160	cis	lesional skin	skin_eQTL
rs6454471	SNHG5	cis	Esophagus Mucosa	GTEx
rs6454471	SNHG5	cis	Whole Blood	GTEx
rs6454471	SNHG5	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86176800-86242600	Weak transcription	Gastric	stomach
2	chr6:86192800-86221400	Weak transcription	Brain Substantia Nigra	brain
3	chr6:86193000-86221200	Weak transcription	A549	lung
4	chr6:86193400-86219800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:86195000-86219800	Weak transcription	Brain Angular Gyrus	brain
6	chr6:86196800-86221600	Weak transcription	Spleen	Spleen
7	chr6:86199600-86219400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:86200000-86219200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:86200200-86219400	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:86200600-86220400	Weak transcription	Psoas Muscle	Psoas
11	chr6:86200600-86221800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:86201000-86216600	Weak transcription	Left Ventricle	heart
13	chr6:86201600-86218800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:86202800-86218800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:86203400-86219800	Weak transcription	NHLF	lung
16	chr6:86205200-86217600	Weak transcription	HSMMtube	muscle
17	chr6:86205200-86219600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:86206000-86215200	Weak transcription	NHDF-Ad	bronchial
19	chr6:86207000-86221600	Weak transcription	Lung	lung
20	chr6:86207200-86217600	Weak transcription	Fetal Intestine Large	intestine
21	chr6:86207200-86219400	Weak transcription	Osteobl	bone
22	chr6:86207200-86219800	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:86207200-86221200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:86207200-86221600	Weak transcription	Brain Germinal Matrix	brain
25	chr6:86207200-86238400	Weak transcription	Esophagus	oesophagus
26	chr6:86207400-86217600	Weak transcription	Placenta	Placenta
27	chr6:86207400-86219200	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:86207400-86219400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:86207400-86219400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:86207400-86219600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:86207400-86221400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:86207400-86221600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:86207400-86221600	Weak transcription	Aorta	Aorta
34	chr6:86207400-86221600	Weak transcription	Fetal Stomach	stomach
35	chr6:86207600-86219400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:86207600-86219400	Weak transcription	Fetal Brain Male	brain
37	chr6:86208400-86219400	Weak transcription	Fetal Brain Female	brain
38	chr6:86208600-86221000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:86208800-86219400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
41	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
42	chr6:86209000-86215000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:86209000-86216000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:86209000-86217600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:86209000-86218800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr6:86209000-86219200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:86209000-86219200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr6:86209000-86219800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:86209000-86219800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:86209000-86221200	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links