Variant report

Variant	rs6669532
Chromosome Location	chr1:246840366-246840367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11586702	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117791	1.00[ASN][1000 genomes]
rs12119414	1.00[ASN][1000 genomes]
rs12121655	1.00[ASN][1000 genomes]
rs12122261	1.00[ASN][1000 genomes]
rs12126135	1.00[ASN][1000 genomes]
rs12130507	1.00[ASN][1000 genomes]
rs12134535	1.00[ASN][1000 genomes]
rs12728036	1.00[ASN][1000 genomes]
rs12728813	1.00[ASN][1000 genomes]
rs12734241	1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes]
rs12750060	1.00[ASN][1000 genomes]
rs34385126	1.00[ASN][1000 genomes]
rs34471048	1.00[ASN][1000 genomes]
rs34695209	1.00[ASN][1000 genomes]
rs35795797	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852409	1.00[ASN][1000 genomes]
rs61852424	1.00[ASN][1000 genomes]
rs61852425	1.00[ASN][1000 genomes]
rs6687128	1.00[ASN][1000 genomes]
rs6701305	1.00[ASN][1000 genomes]
rs6704469	1.00[ASN][1000 genomes]
rs9426208	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426254	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1010316	chr1:246686301-246840960	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv535414	chr1:246686301-246840960	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv528615	chr1:246708467-246843315	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1005214	chr1:246730885-246841107	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1002595	chr1:246774036-246846548	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1007194	chr1:246813090-246855424	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6669532	ZNF496	cis	parietal	SCAN
rs6669532	OR2L2	cis	parietal	SCAN
rs6669532	OR2L8	cis	parietal	SCAN
rs6669532	OR2M4	cis	parietal	SCAN
rs6669532	OR2L13	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246801600-246842800	Weak transcription	Fetal Kidney	kidney
2	chr1:246811800-246841000	Weak transcription	Hela-S3	cervix
3	chr1:246817800-246842600	Weak transcription	HSMMtube	muscle
4	chr1:246822200-246845200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:246822400-246843000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:246825600-246843000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:246829400-246844000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:246829600-246843000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:246829600-246845200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:246829800-246842400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:246829800-246842800	Weak transcription	HSMM	muscle
12	chr1:246829800-246843000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:246829800-246843400	Weak transcription	NH-A	brain
14	chr1:246829800-246844400	Weak transcription	Spleen	Spleen
15	chr1:246829800-246845200	Weak transcription	Fetal Lung	lung
16	chr1:246829800-246845200	Weak transcription	Ovary	ovary
17	chr1:246829800-246853000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:246830000-246842600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:246830000-246842800	Weak transcription	Brain Angular Gyrus	brain
20	chr1:246830000-246842800	Weak transcription	Psoas Muscle	Psoas
21	chr1:246830200-246843400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:246830200-246853000	Weak transcription	Fetal Brain Female	brain
23	chr1:246830400-246841000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:246830400-246842400	Weak transcription	NHLF	lung
25	chr1:246831400-246842600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:246832400-246844000	Weak transcription	Right Ventricle	heart
27	chr1:246832400-246853000	Weak transcription	Thymus	Thymus
28	chr1:246832400-246856400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:246832600-246841000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:246832600-246841400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:246832600-246842400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:246832600-246845000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:246832800-246841000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:246833000-246842400	Weak transcription	NHDF-Ad	bronchial
35	chr1:246833000-246842800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:246833200-246842200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:246833200-246842400	Weak transcription	Fetal Stomach	stomach
38	chr1:246833200-246842600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:246833200-246842600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:246833200-246843200	Weak transcription	Lung	lung
41	chr1:246833400-246842800	Weak transcription	Left Ventricle	heart
42	chr1:246833400-246843200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:246833400-246845200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:246833600-246843600	Weak transcription	Brain Substantia Nigra	brain
45	chr1:246833800-246842800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:246833800-246845200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:246833800-246850000	Weak transcription	Primary T cells from cord blood	blood
48	chr1:246834000-246841000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:246834000-246844400	Weak transcription	Adipose Nuclei	Adipose
50	chr1:246834000-246845000	Weak transcription	Osteobl	bone

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