Variant report

Variant	rs4806303
Chromosome Location	chr19:36745760-36745761
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10403738	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs10407850	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs10416509	0.87[CEU][hapmap];0.92[CHB][hapmap]
rs10416742	0.90[CHB][hapmap]
rs10416925	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs12459248	0.81[AMR][1000 genomes]
rs12459704	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs12460466	0.85[AMR][1000 genomes]
rs12461077	0.82[CHB][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12462725	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12463157	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17206379	0.83[CHB][hapmap]
rs2271842	1.00[CHB][hapmap]
rs28414272	0.87[AMR][1000 genomes]
rs28528757	0.85[AMR][1000 genomes]
rs2857	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2945955	1.00[CHB][hapmap]
rs2945989	0.83[CHB][hapmap]
rs3098393	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs4806284	0.88[CEU][hapmap];0.92[CHB][hapmap]
rs4806293	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4806295	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs55697131	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56316708	0.81[AMR][1000 genomes]
rs58395495	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59026641	0.81[AMR][1000 genomes]
rs62113146	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62113148	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62113149	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62113151	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62113152	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7251745	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs73040107	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73040113	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73040148	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73041817	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8106210	1.00[YRI][hapmap]
rs8111860	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs8113088	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv9715	chr19:36729688-36811749	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1063208	chr19:36743461-36847486	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv961212	chr19:36744378-36801298	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv960831	chr19:36744378-36813769	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4806303	LINC00665	cis	Muscle Skeletal	GTEx
rs4806303	CTD-3162L10.1	cis	Nerve Tibial	GTEx
rs4806303	LINC00665	cis	Nerve Tibial	GTEx
rs4806303	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs4806303	ZNF545	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36730400-36748400	Weak transcription	HSMMtube	muscle
2	chr19:36736200-36746200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:36737400-36747800	Weak transcription	Brain Anterior Caudate	brain
4	chr19:36737400-36747800	Weak transcription	Brain Substantia Nigra	brain
5	chr19:36737400-36748000	Weak transcription	Ovary	ovary
6	chr19:36737600-36746000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr19:36737600-36746200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:36737600-36747800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr19:36737600-36747800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:36737600-36747800	Weak transcription	Brain Hippocampus Middle	brain
11	chr19:36738000-36747800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:36739200-36746200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:36739200-36746800	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:36739600-36756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:36742200-36746200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:36743000-36746000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr19:36744800-36748000	ZNF genes & repeats	Fetal Brain Female	brain
18	chr19:36745200-36746000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:36745200-36746800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr19:36745400-36746000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:36745400-36748000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
22	chr19:36745400-36749200	ZNF genes & repeats	Pancreas	Pancrea
23	chr19:36745600-36746400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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