Variant report

Variant	rs961386
Chromosome Location	chr4:90732803-90732804
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10516846	0.83[YRI][hapmap];0.95[AFR][1000 genomes]
rs10516847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12233696	1.00[CEU][hapmap];0.81[AFR][1000 genomes]
rs12502730	1.00[CEU][hapmap]
rs12640573	0.82[YRI][hapmap]
rs1442132	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs17016074	1.00[YRI][hapmap]
rs17016083	0.81[AFR][1000 genomes]
rs17016100	1.00[YRI][hapmap]
rs17016124	0.93[AFR][1000 genomes]
rs17016126	0.86[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs17016188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17016193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17016196	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17016235	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2298727	1.00[ASN][1000 genomes]
rs2298728	1.00[ASN][1000 genomes]
rs2870027	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34164595	0.98[ASN][1000 genomes]
rs34238791	0.98[ASN][1000 genomes]
rs34351491	0.80[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs34356244	0.93[AFR][1000 genomes]
rs35540244	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35683448	0.81[AFR][1000 genomes]
rs35897584	1.00[ASN][1000 genomes]
rs35921673	0.88[AFR][1000 genomes]
rs3729594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775435	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775437	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775442	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3775444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775453	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796662	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796667	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3822088	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3822091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3857060	1.00[YRI][hapmap]
rs3898322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58877857	0.93[AFR][1000 genomes]
rs6532190	0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs6532200	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6825073	0.95[AFR][1000 genomes]
rs6842093	0.80[MKK][hapmap];1.00[YRI][hapmap]
rs72657741	0.92[AFR][1000 genomes]
rs7699596	0.95[AFR][1000 genomes]
rs894278	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs961386	FAM190A	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90706400-90733800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:90709800-90735400	Weak transcription	Ovary	ovary
3	chr4:90711800-90734000	Weak transcription	Dnd41	blood
4	chr4:90714600-90734000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:90714800-90740400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr4:90718800-90748000	Weak transcription	Brain Angular Gyrus	brain
7	chr4:90719000-90747600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:90722200-90751800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:90722400-90741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:90722600-90741400	Weak transcription	HMEC	breast
11	chr4:90723000-90741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:90724800-90733000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:90725600-90735400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:90727000-90743200	Weak transcription	Fetal Lung	lung
15	chr4:90729000-90741600	Weak transcription	NHEK	skin
16	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:90730800-90757000	Weak transcription	Fetal Stomach	stomach
18	chr4:90731400-90734200	Strong transcription	HUVEC	blood vessel
19	chr4:90731600-90743000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:90731800-90734400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:90732600-90734800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:90732600-90741200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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