Variant report

Variant	rs17751557
Chromosome Location	chr4:87834607-87834608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87831738..87834823-chr4:87927716..87932272,4	K562	blood:
2	chr4:87834231..87835806-chr4:87836450..87839189,2	K562	blood:
3	chr4:87833323..87835057-chr4:87926520..87929216,2	K562	blood:
4	chr4:87832559..87834802-chr4:87929759..87932272,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC10A6-1	chr4:87834419-87834986	NONHSAT097288

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10011798	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs10015121	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs10015639	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs10050311	0.93[CEU][hapmap]
rs1010902	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1010903	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10516786	0.93[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10516788	0.80[TSI][hapmap]
rs11097124	0.86[EUR][1000 genomes]
rs1447994	0.81[EUR][1000 genomes]
rs17012072	0.85[CEU][hapmap]
rs17012170	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17012200	0.93[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17012213	0.95[EUR][1000 genomes]
rs17012216	0.95[EUR][1000 genomes]
rs17012234	0.80[TSI][hapmap]
rs17694112	0.87[CEU][hapmap]
rs17701999	0.80[TSI][hapmap]
rs17751427	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985944	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2053771	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2121871	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs2287147	0.87[CEU][hapmap]
rs4693153	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693154	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693795	0.93[CEU][hapmap];0.84[CHB][hapmap];0.96[EUR][1000 genomes]
rs55698195	0.90[EUR][1000 genomes]
rs55831707	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55851914	0.95[EUR][1000 genomes]
rs56201068	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61651372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531941	0.93[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6819155	0.83[TSI][hapmap]
rs6846822	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs72667703	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72667705	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72667716	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667721	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667724	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667727	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72667735	0.95[EUR][1000 genomes]
rs72667736	0.95[EUR][1000 genomes]
rs72667737	0.95[EUR][1000 genomes]
rs72667739	0.95[EUR][1000 genomes]
rs72667741	0.93[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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv980228	chr4:87834452-87845024	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87825600-87838800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:87825600-87846000	Weak transcription	Gastric	stomach
3	chr4:87825600-87849400	Weak transcription	Lung	lung
4	chr4:87825600-87849400	Weak transcription	Spleen	Spleen
5	chr4:87825800-87839400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:87825800-87843600	Weak transcription	Brain Anterior Caudate	brain
7	chr4:87825800-87854800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:87825800-87854800	Weak transcription	Right Ventricle	heart
9	chr4:87825800-87855200	Weak transcription	Fetal Stomach	stomach
10	chr4:87826000-87852400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:87826200-87841000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:87826200-87843000	Weak transcription	Liver	Liver
13	chr4:87826200-87843400	Weak transcription	Brain Substantia Nigra	brain
14	chr4:87829200-87839800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:87829800-87855000	Weak transcription	Aorta	Aorta
16	chr4:87830200-87849600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:87830200-87855200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:87830400-87847600	Weak transcription	Thymus	Thymus
19	chr4:87830400-87847800	Weak transcription	Psoas Muscle	Psoas
20	chr4:87830400-87849400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:87830400-87854600	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:87830600-87839400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:87830600-87839400	Weak transcription	Adipose Nuclei	Adipose
24	chr4:87830600-87843000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:87830600-87843400	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:87830600-87843400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:87830600-87845600	Weak transcription	Left Ventricle	heart
28	chr4:87831000-87855000	Weak transcription	Fetal Lung	lung
29	chr4:87831400-87854400	Weak transcription	Fetal Heart	heart
30	chr4:87831400-87854800	Weak transcription	Right Atrium	heart
31	chr4:87831800-87840200	Weak transcription	Primary B cells from cord blood	blood
32	chr4:87832200-87854800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:87832800-87840200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:87833000-87837000	Weak transcription	Placenta	Placenta
35	chr4:87833000-87838600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr4:87833000-87839600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:87833800-87838800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:87834200-87835400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:87834400-87835200	Strong transcription	Fetal Intestine Small	intestine
40	chr4:87834400-87835200	Strong transcription	Pancreas	Pancrea
41	chr4:87834600-87834800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links