Variant report

Variant	rs6800578
Chromosome Location	chr3:143512737-143512738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11706302	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711676	0.84[EUR][1000 genomes]
rs11714765	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11718136	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719982	0.80[AMR][1000 genomes]
rs11720499	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11721078	0.88[CHB][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs11919889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11919894	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11924528	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11924554	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12233446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16854291	0.83[CEU][hapmap]
rs16854322	0.83[CEU][hapmap]
rs16854336	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1868180	0.83[CEU][hapmap]
rs1985503	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2121775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34283894	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4589932	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4632538	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55936201	0.84[EUR][1000 genomes]
rs56166522	0.80[AMR][1000 genomes]
rs56969315	0.84[EUR][1000 genomes]
rs6807571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143492400-143513000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:143494800-143515600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:143494800-143515800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:143499600-143512800	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143505800-143513800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:143505800-143514800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:143505800-143514800	Weak transcription	Lung	lung
8	chr3:143505800-143515400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:143505800-143525800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:143506000-143512800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:143506000-143513200	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:143506000-143514800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:143506000-143521200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:143506400-143514400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:143506400-143514800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:143506400-143515800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:143506600-143513000	Weak transcription	Fetal Lung	lung
18	chr3:143506600-143514600	Weak transcription	Brain Anterior Caudate	brain
19	chr3:143509800-143514800	Weak transcription	Esophagus	oesophagus
20	chr3:143510200-143513200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:143510600-143513000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:143510600-143515000	Weak transcription	Small Intestine	intestine
23	chr3:143510800-143513600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:143510800-143514000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr3:143511800-143513000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:143511800-143513600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:143511800-143514400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:143512000-143529200	Weak transcription	Primary B cells from cord blood	blood
29	chr3:143512400-143513200	Enhancers	Fetal Stomach	stomach
30	chr3:143512400-143513800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:143512400-143513800	Enhancers	Colon Smooth Muscle	Colon
32	chr3:143512600-143512800	Enhancers	HSMM	muscle
33	chr3:143512600-143513000	Enhancers	Adipose Nuclei	Adipose
34	chr3:143512600-143513000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:143512600-143513400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr3:143512600-143513600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr3:143512600-143513800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:143512600-143514000	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:143512600-143515200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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