Variant report

Variant	rs12041704
Chromosome Location	chr1:185240474-185240475
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	chr1:185234057..185236826-chr1:185238378..185241484,4	K562	blood:

Variant related genes	Relation type
ENSG00000252612	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10174	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10752947	0.84[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs10798002	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798003	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs10911693	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10911700	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs10911702	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10911704	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10911708	0.81[EUR][1000 genomes]
rs12026391	0.87[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118722	0.81[ASN][1000 genomes]
rs12120377	0.83[ASN][1000 genomes]
rs12135769	0.96[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs12136040	0.92[EUR][1000 genomes]
rs1336752	0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1336753	0.98[EUR][1000 genomes]
rs17641003	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1889976	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2095610	0.85[EUR][1000 genomes]
rs2152707	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2224027	0.81[CEU][hapmap]
rs2378909	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378910	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34611062	0.90[EUR][1000 genomes]
rs57977436	0.91[EUR][1000 genomes]
rs6682891	0.87[EUR][1000 genomes]
rs6685627	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7123	0.89[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726567	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7535064	0.83[ASN][1000 genomes]
rs7537341	0.89[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs7539575	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7542721	0.92[EUR][1000 genomes]
rs7545878	0.81[CEU][hapmap]
rs7550586	0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs883753	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951428	0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12041704	IVNS1ABP	Cis_1M	lymphoblastoid	RTeQTL
rs12041704	RP4-635A23.4	cis	Artery Tibial	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185193800-185263600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:185210600-185250400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:185218800-185269400	Weak transcription	Pancreas	Pancrea
4	chr1:185227000-185247400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:185227800-185262000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:185228800-185250400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:185230400-185247000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:185231000-185263400	Weak transcription	Fetal Kidney	kidney
9	chr1:185231800-185249200	Weak transcription	Primary T cells from cord blood	blood
10	chr1:185234000-185253200	Weak transcription	Fetal Heart	heart
11	chr1:185235000-185261800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:185235200-185256800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:185235400-185265400	Weak transcription	Brain Substantia Nigra	brain
14	chr1:185236600-185265600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:185237000-185248000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:185237800-185240800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:185237800-185241000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:185238800-185253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:185239000-185247200	Weak transcription	Ovary	ovary
20	chr1:185239600-185247400	Weak transcription	Brain Angular Gyrus	brain
21	chr1:185239600-185249600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:185239600-185262000	Weak transcription	HSMMtube	muscle
23	chr1:185239800-185250400	Weak transcription	Liver	Liver
24	chr1:185239800-185262000	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:185239800-185263800	Weak transcription	Brain Anterior Caudate	brain
26	chr1:185240000-185247400	Weak transcription	Primary B cells from cord blood	blood
27	chr1:185240000-185265800	Weak transcription	Fetal Lung	lung
28	chr1:185240200-185267200	Weak transcription	Gastric	stomach
29	chr1:185240400-185247200	Weak transcription	Left Ventricle	heart
30	chr1:185240400-185268800	Weak transcription	Aorta	Aorta

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