Variant report

Variant	rs10488942
Chromosome Location	chr4:106469628-106469629
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr4:106469621-106469900	A549	lung:	n/a	n/a
2	JUND	chr4:106469465-106470144	SK-N-SH	brain:	n/a	n/a
3	JUND	chr4:106469458-106470119	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr4:106468777-106470221	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr4:106469428-106470160	SK-N-SH	brain:	n/a	n/a
6	FOSL2	chr4:106469579-106470056	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr4:106469441-106470228	SK-N-SH	brain:	n/a	n/a
8	EP300	chr4:106469609-106470065	SK-N-SH_RA	brain:	n/a	n/a
9	FOSL2	chr4:106469493-106470113	SK-N-SH	brain:	n/a	n/a
10	EP300	chr4:106469606-106470040	SK-N-SH_RA	brain:	n/a	n/a
11	TEAD4	chr4:106469472-106470097	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr4:106468824-106470155	SK-N-SH	brain:	n/a	n/a
13	TEAD4	chr4:106469610-106470046	H1-hESC	embryonic stem cell:	n/a	n/a
14	PBX3	chr4:106469499-106470253	SK-N-SH	brain:	n/a	n/a
15	EP300	chr4:106468814-106470014	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr4:106468794-106470246	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr4:106469596-106470095	SK-N-SH	brain:	n/a	n/a
18	PBX3	chr4:106469542-106470211	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ARHGEF38	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10001434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10001614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10007801	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10014771	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10016616	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10024863	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs10025663	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032241	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470907	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11938316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1490596	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17035687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17035704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17035711	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2107046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2158202	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28380268	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28422499	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28444199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28462162	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28634484	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28678184	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28687111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28707788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28754790	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3948725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56068525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6816893	0.87[CEU][hapmap];0.98[EUR][1000 genomes]
rs6817444	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6825245	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858204	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs730207	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs730208	0.87[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs730850	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7661571	0.87[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1005011	chr4:106461690-106496019	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1013019	chr4:106461690-106501412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv524424	chr4:106466128-106491511	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv461610	chr4:106466128-106491511	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv595008	chr4:106466128-106491511	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv517837	chr4:106466588-106502513	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106464600-106471200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:106466000-106471400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:106466400-106470600	Weak transcription	Fetal Intestine Small	intestine
4	chr4:106466600-106471400	Weak transcription	Fetal Intestine Large	intestine
5	chr4:106466600-106471600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:106466600-106472600	Weak transcription	Fetal Kidney	kidney
7	chr4:106467600-106471600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:106468000-106472600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:106468800-106470000	Enhancers	NHEK	skin
10	chr4:106469000-106470200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:106469000-106470200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:106469000-106470200	Enhancers	HMEC	breast
13	chr4:106469200-106470200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:106469400-106470000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:106469400-106470000	Enhancers	HSMM	muscle
16	chr4:106469400-106470200	Enhancers	A549	lung
17	chr4:106469600-106469800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:106469600-106470000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr4:106469600-106470000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links