Variant report

Variant	rs4235826
Chromosome Location	chr6:86184890-86184891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86182269..86185102-chr6:86204566..86206145,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10944133	0.82[ASN][1000 genomes]
rs12199873	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12205013	0.83[ASN][1000 genomes]
rs1590281	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1885607	0.84[AFR][1000 genomes]
rs2065114	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2208725	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2229523	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2475790	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2475791	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2758840	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2758844	0.83[ASN][1000 genomes]
rs2758846	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2758847	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2783171	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2842601	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2842602	0.83[ASN][1000 genomes]
rs2842604	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2842607	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2842608	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2842609	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2842612	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2842613	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3812133	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4235827	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282381	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4304137	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4351223	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4373337	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4419647	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4441928	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4501401	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4562107	0.83[ASN][1000 genomes]
rs4579322	0.85[CHB][hapmap]
rs4593336	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs4706240	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4707207	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707209	0.91[ASN][1000 genomes]
rs6454468	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6454469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6454471	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]
rs6922	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6926049	0.90[ASN][1000 genomes]
rs6931295	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7452605	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7739563	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7746065	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7765636	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7768065	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7770359	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9294337	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9344532	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9351065	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9353318	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9362230	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9362233	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9444349	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450272	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450282	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs9450287	0.82[EUR][1000 genomes]
rs9450290	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4235826	SNHG5	cis	Muscle Skeletal	GTEx
rs4235826	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs4235826	SNHG5	cis	multi-tissue	Pritchard
rs4235826	SNHG5	cis	Esophagus Mucosa	GTEx
rs4235826	C6orf160	cis	lesional skin	skin_eQTL
rs4235826	SNHG5	cis	Nerve Tibial	GTEx
rs4235826	SNHG5	cis	Heart Left Ventricle	GTEx
rs4235826	C6orf160	cis	normal skin	skin_eQTL
rs4235826	SNHG5	cis	lung	GTEx
rs4235826	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs4235826	SNHG5	cis	Thyroid	GTEx
rs4235826	SNHG5	cis	Artery Tibial	GTEx
rs4235826	SNHG5	cis	Whole Blood	GTEx
rs4235826	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs4235826	C6orf160	cis	uninvolved skin	skin_eQTL
rs4235826	SNHG5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86171800-86185200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:86171800-86186000	Weak transcription	Fetal Stomach	stomach
3	chr6:86171800-86187600	Weak transcription	Colonic Mucosa	Colon
4	chr6:86172200-86186000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:86172400-86192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:86175600-86191800	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:86176200-86187000	Strong transcription	Liver	Liver
8	chr6:86176200-86192400	Weak transcription	A549	lung
9	chr6:86176200-86192600	Weak transcription	HepG2	liver
10	chr6:86176600-86191400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:86176800-86242600	Weak transcription	Gastric	stomach
12	chr6:86178800-86206800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:86179200-86185600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:86179400-86186000	Weak transcription	Lung	lung
15	chr6:86180000-86191600	Strong transcription	HSMM	muscle
16	chr6:86180400-86185800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:86181000-86186800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:86182000-86185200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:86182000-86192200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:86182200-86186000	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:86183000-86185800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:86183000-86185800	Weak transcription	Aorta	Aorta
23	chr6:86183200-86186000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:86183200-86190400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:86183200-86190600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr6:86183200-86192200	Weak transcription	HUVEC	blood vessel
27	chr6:86183400-86185800	Weak transcription	Ovary	ovary
28	chr6:86183600-86185200	Weak transcription	NHEK	skin
29	chr6:86183600-86188200	Strong transcription	NH-A	brain
30	chr6:86183800-86185000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:86183800-86188600	Strong transcription	NHDF-Ad	bronchial
32	chr6:86183800-86190200	Weak transcription	HSMMtube	muscle
33	chr6:86183800-86190600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:86183800-86191600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:86183800-86192600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr6:86184000-86189600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:86184200-86190200	Strong transcription	HMEC	breast
38	chr6:86184200-86191000	Strong transcription	Osteobl	bone
39	chr6:86184200-86192200	Weak transcription	Hela-S3	cervix
40	chr6:86184400-86185200	Strong transcription	Primary T cells from cord blood	blood
41	chr6:86184600-86185800	Weak transcription	Placenta	Placenta
42	chr6:86184600-86190200	Strong transcription	NHLF	lung
43	chr6:86184800-86185200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:86184800-86185400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:86184800-86187200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links