Variant report

Variant	rs7595040
Chromosome Location	chr2:50705043-50705044
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	chr2:50698680..50701343-chr2:50702519..50705361,2	K562	blood:
2	chr2:50699843..50701598-chr2:50702519..50705507,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1006138	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1014430	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10168080	0.81[ASN][1000 genomes]
rs10168838	0.84[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10176959	0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10183541	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10184537	1.00[YRI][hapmap]
rs10187846	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10190305	0.81[ASN][1000 genomes]
rs10191072	0.83[ASN][1000 genomes]
rs1019318	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10199840	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs10207057	0.83[ASN][1000 genomes]
rs10210592	0.82[ASN][1000 genomes]
rs10211193	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1030050	0.81[ASN][1000 genomes]
rs13012186	0.82[ASN][1000 genomes]
rs13034257	0.82[ASN][1000 genomes]
rs1879318	0.92[CHD][hapmap]
rs1984957	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2041868	0.81[ASN][1000 genomes]
rs2041869	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2066948	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs2111065	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2111066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2111069	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2160448	1.00[ASW][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2160449	0.81[ASN][1000 genomes]
rs2216171	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6545172	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545173	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6545174	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545175	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6545176	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs6545177	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6545178	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6707531	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs6713061	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6722389	0.83[ASN][1000 genomes]
rs6732076	0.81[ASN][1000 genomes]
rs6753552	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7564428	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7566514	0.83[ASN][1000 genomes]
rs759503	0.91[ASN][1000 genomes]
rs759505	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs759506	0.85[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv934040	chr2:50681850-50711452	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7595040	GPR75	cis	parietal	SCAN
rs7595040	FBXO11	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50691200-50711600	Weak transcription	Fetal Brain Female	brain
2	chr2:50691200-50716000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:50691600-50718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:50692600-50705400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:50695600-50709400	Weak transcription	Brain Germinal Matrix	brain
6	chr2:50699000-50742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:50704400-50718600	Weak transcription	Fetal Brain Male	brain
8	chr2:50704800-50705200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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