Variant report

Variant	rs4507229
Chromosome Location	chr3:112023442-112023443
allele	C/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	CTCF	chr3:112023420-112023570	HL-60	blood:	n/a	n/a
2	CTCF	chr3:112023400-112023550	HAc	cerebellar:	n/a	n/a

Variant related genes	Relation type
ENSG00000239482	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10511310	1.00[CHB][hapmap]
rs10804498	1.00[ASN][1000 genomes]
rs10934163	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10934164	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10934165	1.00[ASN][1000 genomes]
rs11709101	1.00[ASN][1000 genomes]
rs11717777	1.00[ASN][1000 genomes]
rs11720514	1.00[ASN][1000 genomes]
rs11923402	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926389	1.00[CHB][hapmap]
rs12489470	1.00[CHB][hapmap]
rs12489616	1.00[CHB][hapmap]
rs12497979	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12636943	1.00[CHB][hapmap]
rs13063452	1.00[CHB][hapmap]
rs13064242	1.00[CHB][hapmap]
rs13084103	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1317295	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317658	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316383	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388858	1.00[CHB][hapmap]
rs1388859	1.00[CHB][hapmap]
rs1492479	1.00[ASN][1000 genomes]
rs1492489	1.00[CHB][hapmap]
rs17446282	1.00[CHB][hapmap]
rs17513880	1.00[ASN][1000 genomes]
rs2399419	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399422	0.81[CEU][hapmap]
rs2633546	1.00[ASN][1000 genomes]
rs2683891	1.00[ASN][1000 genomes]
rs2683892	1.00[ASN][1000 genomes]
rs28615303	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234409	1.00[CHB][hapmap]
rs4234411	1.00[CHB][hapmap]
rs4321508	1.00[CHB][hapmap]
rs4347976	1.00[CHB][hapmap]
rs4434123	1.00[CHB][hapmap]
rs4538347	1.00[CHB][hapmap]
rs4622877	1.00[ASN][1000 genomes]
rs4638935	1.00[CHB][hapmap]
rs4682393	1.00[ASN][1000 genomes]
rs4682400	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56008438	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56294743	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56364691	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	1.00[ASN][1000 genomes]
rs60949597	1.00[ASN][1000 genomes]
rs62262366	1.00[ASN][1000 genomes]
rs62262408	1.00[ASN][1000 genomes]
rs62262411	1.00[ASN][1000 genomes]
rs62264125	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264128	1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62278765	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278768	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278769	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278770	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278771	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278843	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438072	1.00[ASN][1000 genomes]
rs6766013	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6781844	1.00[CHB][hapmap]
rs6787323	1.00[CHB][hapmap]
rs6789875	1.00[CHB][hapmap]
rs6795820	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797177	1.00[CHB][hapmap]
rs6801795	1.00[CHB][hapmap]
rs6804836	1.00[CHB][hapmap]
rs6805112	1.00[CHB][hapmap]
rs6805397	1.00[CHB][hapmap]
rs73223638	1.00[ASN][1000 genomes]
rs7431999	1.00[CHB][hapmap]
rs7609904	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7612748	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7621431	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7625249	1.00[CHB][hapmap]
rs7631673	1.00[ASN][1000 genomes]
rs7636107	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7637676	1.00[CHB][hapmap]
rs7637682	1.00[CHB][hapmap]
rs7650962	1.00[ASN][1000 genomes]
rs7651121	1.00[ASN][1000 genomes]
rs9288939	1.00[CHB][hapmap]
rs9288942	1.00[CHB][hapmap]
rs9810170	1.00[CHB][hapmap]
rs9810421	1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816969	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818407	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823824	1.00[ASN][1000 genomes]
rs9829698	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837134	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9843666	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9851760	1.00[ASN][1000 genomes]
rs9853669	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855755	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9871088	1.00[ASN][1000 genomes]
rs9871492	1.00[CHB][hapmap]

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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv967052	chr3:112020436-112027937	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4507229	C6orf106	trans	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112021400-112025200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:112021600-112023600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:112021800-112023600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:112021800-112023600	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr3:112021800-112023600	Enhancers	Lung	lung
6	chr3:112021800-112023600	Active TSS	Psoas Muscle	Psoas
7	chr3:112022000-112023600	Active TSS	Fetal Intestine Small	intestine
8	chr3:112022200-112023600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:112022200-112023600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr3:112022400-112023600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr3:112022600-112023600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:112022600-112023600	Active TSS	Brain Substantia Nigra	brain
13	chr3:112022600-112023600	Enhancers	Small Intestine	intestine
14	chr3:112022800-112023600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:112022800-112023600	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr3:112022800-112023800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:112022800-112026400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:112023000-112023600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:112023000-112023600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:112023000-112023600	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr3:112023000-112023600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr3:112023000-112023600	Flanking Active TSS	Fetal Brain Male	brain
23	chr3:112023000-112023600	Flanking Active TSS	Fetal Lung	lung
24	chr3:112023000-112023600	Flanking Active TSS	Right Atrium	heart
25	chr3:112023000-112023600	Flanking Active TSS	NH-A	brain
26	chr3:112023000-112023600	Flanking Active TSS	Osteobl	bone
27	chr3:112023000-112024000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:112023000-112024000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:112023000-112024200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:112023000-112024600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:112023000-112024600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:112023000-112024800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr3:112023200-112023600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:112023200-112023600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:112023200-112023600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr3:112023200-112023600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr3:112023200-112023600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:112023200-112023600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr3:112023200-112023600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:112023200-112023600	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr3:112023200-112023600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:112023200-112023600	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr3:112023200-112023800	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr3:112023200-112023800	Enhancers	Fetal Heart	heart
45	chr3:112023200-112024000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:112023200-112024000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:112023200-112024000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:112023200-112024200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr3:112023200-112024200	Enhancers	Fetal Intestine Large	intestine
50	chr3:112023200-112024200	Enhancers	Fetal Thymus	thymus

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