Variant report

Variant	rs6770719
Chromosome Location	chr3:121526849-121526850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10934560	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10934568	0.81[JPT][hapmap]
rs12489511	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490565	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067629	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs1492177	0.90[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs17849995	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1873645	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs1919552	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1919557	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2001391	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs2070179	0.90[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs2141614	1.00[JPT][hapmap]
rs2331963	0.83[MEX][hapmap]
rs2332056	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs2700424	0.81[JPT][hapmap]
rs2840143	0.90[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs34227248	0.86[ASN][1000 genomes]
rs34920680	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34980632	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35713885	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36022362	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3817599	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs4482697	0.83[MEX][hapmap]
rs4676690	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4676751	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4676754	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57420306	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59740137	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438661	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6771716	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774164	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6776703	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6791510	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6802033	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs6803839	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6807711	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs73179983	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73181839	0.89[ASN][1000 genomes]
rs7375038	0.90[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7429247	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs7611913	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs7646346	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7646585	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs7652239	0.89[ASN][1000 genomes]
rs9289172	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs9289173	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs953730	0.80[GIH][hapmap]
rs9681049	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9681209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9809114	0.90[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs9812411	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs9829053	0.80[EUR][1000 genomes]
rs9864907	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs9876021	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv933676	chr3:121517764-121528304	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6770719	MUC13	cis	cerebellum	SCAN
rs6770719	SLC15A2	cis	parietal	SCAN
rs6770719	ADPRH	cis	parietal	SCAN
rs6770719	SLC15A2	cis	cerebellum	SCAN
rs6770719	HCLS1	Cis_1M	lymphoblastoid	RTeQTL
rs6770719	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:121489800-121529800	Weak transcription	Aorta	Aorta
3	chr3:121490000-121529800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:121490000-121529800	Weak transcription	Pancreas	Pancrea
5	chr3:121491600-121552600	Weak transcription	NHLF	lung
6	chr3:121494200-121544200	Weak transcription	Fetal Brain Male	brain
7	chr3:121494400-121530000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:121500200-121541400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:121500600-121528200	Weak transcription	Brain Angular Gyrus	brain
10	chr3:121501400-121529800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:121506400-121529800	Weak transcription	Fetal Stomach	stomach
12	chr3:121507000-121529800	Weak transcription	Colonic Mucosa	Colon
13	chr3:121507000-121545400	Weak transcription	Fetal Heart	heart
14	chr3:121507200-121536000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:121508000-121529800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:121508200-121535800	Weak transcription	Psoas Muscle	Psoas
17	chr3:121508400-121529800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:121508400-121529800	Weak transcription	Esophagus	oesophagus
19	chr3:121508400-121536400	Weak transcription	HUVEC	blood vessel
20	chr3:121508600-121529600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:121508600-121529800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:121508600-121529800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:121508600-121529800	Weak transcription	NHEK	skin
24	chr3:121508600-121541400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:121508800-121530000	Weak transcription	Brain Germinal Matrix	brain
26	chr3:121508800-121530200	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:121509000-121529600	Weak transcription	HSMMtube	muscle
28	chr3:121509000-121529800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:121509000-121529800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:121515200-121530200	Weak transcription	Small Intestine	intestine
31	chr3:121518800-121530200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:121519600-121530400	Weak transcription	Right Ventricle	heart
33	chr3:121521200-121527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:121521600-121527800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:121521600-121531600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:121521800-121527000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:121521800-121527600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:121521800-121531600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:121522000-121531200	Strong transcription	Dnd41	blood
40	chr3:121522200-121531200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:121522400-121536600	Weak transcription	Fetal Kidney	kidney
42	chr3:121522600-121527000	Strong transcription	Adipose Nuclei	Adipose
43	chr3:121522800-121528600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:121523000-121531600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:121523200-121531200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:121523200-121534000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:121523400-121527200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:121523400-121527200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:121523400-121528600	Strong transcription	HSMM	muscle
50	chr3:121523600-121527000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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