Variant report

Variant	rs17451111
Chromosome Location	chr4:87274174-87274175
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87273387..87275250-chr4:87290836..87293550,2	K562	blood:

Variant related genes	Relation type
ENSG00000109339	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1031739	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[TSI][hapmap]
rs1460752	0.83[AMR][1000 genomes]
rs17408832	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes]
rs17409478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17409637	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17417758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17449147	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17449582	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2869423	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes]
rs2869433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869434	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35103650	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4299551	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs4521313	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693140	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4693762	0.83[AMR][1000 genomes]
rs4693763	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs4693769	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55724430	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56255533	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57869802	0.86[AMR][1000 genomes]
rs58538747	0.83[AMR][1000 genomes]
rs60753208	0.86[AMR][1000 genomes]
rs62305543	0.84[AMR][1000 genomes]
rs62305546	0.83[AMR][1000 genomes]
rs62307365	0.86[AMR][1000 genomes]
rs62307366	0.86[AMR][1000 genomes]
rs62307367	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62307409	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62307454	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62308361	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62308365	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6827483	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes]
rs72663972	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7376405	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7688651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv934210	chr4:87197339-87325578	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	nsv461574	chr4:87239764-87279096	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv594788	chr4:87239764-87279096	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17451111	SLC6A4	trans	lymphoblastoid	seeQTL
rs17451111	MAPK10	cis	lesional skin	skin_eQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87256200-87275800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:87259200-87274200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:87260400-87277800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:87260800-87277200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:87263800-87276000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:87264000-87277000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:87264200-87277800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:87264400-87280600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:87265600-87278000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:87266200-87278200	Weak transcription	Fetal Kidney	kidney
11	chr4:87267600-87276400	Weak transcription	Fetal Brain Male	brain
12	chr4:87269200-87279400	Weak transcription	Psoas Muscle	Psoas
13	chr4:87269600-87279400	Weak transcription	Ovary	ovary
14	chr4:87270600-87276400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:87270800-87275800	Weak transcription	Fetal Intestine Large	intestine
16	chr4:87270800-87278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:87270800-87279600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:87271200-87274400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:87271200-87275800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:87271200-87277200	Weak transcription	Brain Anterior Caudate	brain
21	chr4:87271400-87274800	Weak transcription	Brain Angular Gyrus	brain
22	chr4:87272000-87276600	Weak transcription	Fetal Brain Female	brain
23	chr4:87272200-87280600	Weak transcription	Adipose Nuclei	Adipose
24	chr4:87272600-87275800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:87272600-87280600	Weak transcription	Fetal Lung	lung
26	chr4:87272800-87278000	Weak transcription	Brain Substantia Nigra	brain
27	chr4:87273000-87274600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr4:87273400-87274400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:87273600-87274200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:87273600-87274400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr4:87273600-87274400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr4:87273600-87274400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:87273800-87274200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr4:87273800-87280600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr4:87274000-87274600	Strong transcription	Brain Hippocampus Middle	brain
36	chr4:87274000-87275400	Strong transcription	Brain Cingulate Gyrus	brain
37	chr4:87274000-87275600	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links