Variant report

Variant	rs6545176
Chromosome Location	chr2:50726324-50726325
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	STAT3	chr2:50726242-50726657	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:50726310-50726510	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
NRXN1	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1006138	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1014430	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10168080	0.93[ASN][1000 genomes]
rs10168838	0.90[JPT][hapmap]
rs10176959	0.86[ASN][1000 genomes]
rs10183541	0.95[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs10187846	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10190305	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10191072	0.94[ASN][1000 genomes]
rs1019318	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs10199840	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs10207057	0.93[ASN][1000 genomes]
rs10210592	0.95[ASN][1000 genomes]
rs10211193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1030050	0.93[ASN][1000 genomes]
rs12713104	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13012186	0.95[ASN][1000 genomes]
rs13034257	0.95[ASN][1000 genomes]
rs1879318	0.80[CHD][hapmap]
rs1984957	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2041868	0.88[ASN][1000 genomes]
rs2041869	0.85[ASN][1000 genomes]
rs2058751	0.88[ASN][1000 genomes]
rs2058752	0.88[ASN][1000 genomes]
rs2066948	0.89[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs2111065	0.85[ASN][1000 genomes]
rs2111066	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs2111069	0.84[ASN][1000 genomes]
rs2160448	1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2160449	0.93[ASN][1000 genomes]
rs2216171	0.85[ASN][1000 genomes]
rs6545172	0.85[ASN][1000 genomes]
rs6545173	0.86[ASN][1000 genomes]
rs6545174	0.89[ASN][1000 genomes]
rs6545175	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6545177	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6545178	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6707531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs6713061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6722389	0.94[ASN][1000 genomes]
rs6732076	0.93[ASN][1000 genomes]
rs6753552	0.90[ASN][1000 genomes]
rs7564428	0.91[ASN][1000 genomes]
rs7566514	0.93[ASN][1000 genomes]
rs7595040	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs759505	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs759506	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1010510	chr2:50649641-51011565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv535694	chr2:50649641-51011565	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv532650	chr2:50675808-51136752	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv491644	chr2:50680795-50892906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv498102	chr2:50680795-50937503	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv2724	chr2:50688876-50734321	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv532651	chr2:50712339-50758351	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv532681	chr2:50715261-51172182	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv933959	chr2:50722885-50858529	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv915896	chr2:50725664-51057797	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv498101	chr2:50725729-50937503	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6545176	RHOQ	cis	parietal	SCAN
rs6545176	GPR75	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50699000-50742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:50719600-50734400	Weak transcription	Fetal Brain Male	brain
3	chr2:50719800-50736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:50723200-50729200	Weak transcription	Brain Germinal Matrix	brain
5	chr2:50724800-50732400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:50724800-50739400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:50724800-50746600	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links