Variant report

Variant	rs12190983
Chromosome Location	chr6:114385035-114385036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10782177	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11967410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11970460	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12201726	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201804	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203341	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207338	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12211751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211928	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12213853	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17191369	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1961955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475621	0.81[CEU][hapmap]
rs2475623	0.80[CEU][hapmap]
rs2475624	0.81[CEU][hapmap]
rs4551200	0.81[CEU][hapmap]
rs62418080	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742134	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7743208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7753206	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9320479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9374432	0.81[CEU][hapmap]
rs9398370	0.81[CEU][hapmap]
rs9481418	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9481421	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9488328	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9488329	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9488334	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12190983	KIAA1919	cis	parietal	SCAN
rs12190983	RFPL4B	cis	cerebellum	SCAN
rs12190983	BET3L	cis	parietal	SCAN
rs12190983	CRY1	trans	lymphoblastoid	seeQTL
rs12190983	ROS1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114370000-114387000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:114370200-114389600	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:114371400-114388200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:114379600-114390400	Weak transcription	HepG2	liver
5	chr6:114380800-114388000	Weak transcription	Psoas Muscle	Psoas
6	chr6:114381200-114386400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:114383400-114390000	Weak transcription	Brain Germinal Matrix	brain
8	chr6:114384000-114389600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:114384200-114385800	Enhancers	Fetal Heart	heart
10	chr6:114384200-114389400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:114384200-114389400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:114384200-114389600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:114384200-114389600	Weak transcription	Brain Substantia Nigra	brain
14	chr6:114384200-114390000	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:114384200-114398200	Weak transcription	Brain Angular Gyrus	brain
16	chr6:114384600-114385200	Enhancers	Brain Anterior Caudate	brain
17	chr6:114384800-114385200	Enhancers	HUVEC	blood vessel
18	chr6:114384800-114385600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:114384800-114385600	Enhancers	HSMM	muscle
20	chr6:114384800-114385800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:114384800-114385800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:114384800-114386000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:114384800-114386400	Enhancers	HSMMtube	muscle
24	chr6:114385000-114385200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:114385000-114385200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr6:114385000-114385200	Enhancers	NHDF-Ad	bronchial
27	chr6:114385000-114385400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:114385000-114385600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:114385000-114385800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:114385000-114385800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:114385000-114385800	Enhancers	NH-A	brain
32	chr6:114385000-114386000	Enhancers	Osteobl	bone
33	chr6:114385000-114386600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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