Variant report

Variant	rs16843978
Chromosome Location	chr3:136106435-136106436
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10513002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067714	0.90[EUR][1000 genomes]
rs16843879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16843991	1.00[CHB][hapmap]
rs17199880	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17199978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17265675	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17266364	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	1.00[CHB][hapmap]
rs35644083	1.00[CHB][hapmap]
rs3872588	1.00[CHB][hapmap]
rs3913715	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931416	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs4125861	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55848312	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56057807	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56095774	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56264828	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336182	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58636237	0.81[EUR][1000 genomes]
rs58641485	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60014495	0.82[EUR][1000 genomes]
rs60270684	0.82[EUR][1000 genomes]
rs6439638	1.00[CHB][hapmap]
rs6439642	1.00[CHB][hapmap]
rs66494666	0.82[EUR][1000 genomes]
rs66637842	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67082054	0.81[EUR][1000 genomes]
rs67230667	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67389407	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67452583	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67525027	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67621498	0.82[EUR][1000 genomes]
rs67663578	0.82[EUR][1000 genomes]
rs67677899	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769582	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773495	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6773604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776841	1.00[CHB][hapmap]
rs67794070	0.82[EUR][1000 genomes]
rs6783337	1.00[CHB][hapmap]
rs67902591	0.81[EUR][1000 genomes]
rs67963055	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67971203	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6800570	1.00[CHB][hapmap]
rs6804194	1.00[CHB][hapmap]
rs6808143	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73224201	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625592	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7644471	1.00[CHB][hapmap]
rs7650075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652176	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833162	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16843978	IL20RB	cis	Artery Tibial	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:136063600-136110600	Weak transcription	Small Intestine	intestine
5	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
6	chr3:136067600-136109000	Weak transcription	HUVEC	blood vessel
7	chr3:136069400-136121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:136069600-136107400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:136069600-136138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:136069600-136139400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:136069800-136106600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:136069800-136118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:136070800-136112200	Weak transcription	Aorta	Aorta
15	chr3:136070800-136121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:136075000-136137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:136075400-136108000	Weak transcription	Fetal Brain Female	brain
18	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
19	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:136081200-136118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:136083200-136111400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:136084400-136123200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:136085600-136116400	Weak transcription	Fetal Intestine Large	intestine
24	chr3:136085800-136116400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:136085800-136139200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:136086000-136112200	Weak transcription	Liver	Liver
28	chr3:136086000-136128400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:136086000-136136000	Weak transcription	HSMM	muscle
30	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:136086400-136116800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:136088400-136121200	Weak transcription	Thymus	Thymus
33	chr3:136092200-136108000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:136093200-136117000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:136094600-136115800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:136095600-136116200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:136095600-136117200	Weak transcription	Placenta	Placenta
38	chr3:136095600-136121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:136095600-136132400	Weak transcription	Left Ventricle	heart
40	chr3:136095600-136132600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:136095600-136134400	Weak transcription	Adipose Nuclei	Adipose
42	chr3:136095600-136137800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:136095800-136116600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:136095800-136118800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:136095800-136121200	Weak transcription	Fetal Thymus	thymus
46	chr3:136095800-136122800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:136095800-136131600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:136095800-136135200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:136095800-136139200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:136096000-136115800	Weak transcription	Dnd41	blood

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