Variant report

Variant	rs6766737
Chromosome Location	chr3:121394749-121394750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10511407	0.82[JPT][hapmap]
rs10934556	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10934557	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934561	0.85[JPT][hapmap]
rs11915822	1.00[ASW][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919421	0.92[ASW][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486456	0.85[JPT][hapmap]
rs12488717	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489110	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489196	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489686	0.82[JPT][hapmap]
rs12491109	0.82[JPT][hapmap]
rs12491671	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491714	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12492214	0.85[JPT][hapmap]
rs12492861	0.82[JPT][hapmap]
rs12493927	1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631803	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636562	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12637265	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574654	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1814668	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1919553	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919554	1.00[ASW][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1919556	1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971281	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2055034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2700413	0.86[GIH][hapmap]
rs2700414	0.85[JPT][hapmap]
rs35674179	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825165	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3805125	0.83[ASW][hapmap];0.82[JPT][hapmap]
rs3805129	0.85[JPT][hapmap]
rs3966063	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4048693	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271407	0.91[EUR][1000 genomes]
rs4610269	0.85[JPT][hapmap]
rs55930520	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55964762	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109033	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56286202	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762575	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6775634	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786605	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798575	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643293	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	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
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6766737	IQCB1	cis	lymphoblastoid	seeQTL
rs6766737	HCLS1	cis	lymphoblastoid	seeQTL
rs6766737	HCLS1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121379400-121402400	Strong transcription	Fetal Intestine Large	intestine
2	chr3:121380000-121402600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:121380200-121397000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:121380400-121396400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:121380400-121396800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:121380400-121402400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:121380400-121402800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:121380400-121406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:121380600-121413800	Weak transcription	Stomach Mucosa	stomach
10	chr3:121381000-121401800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:121381000-121403200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:121381400-121406800	Strong transcription	Duodenum Mucosa	Duodenum
13	chr3:121381600-121396600	Strong transcription	Fetal Thymus	thymus
14	chr3:121381600-121396800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:121381600-121396800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:121381600-121401600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr3:121381600-121402200	Strong transcription	Placenta	Placenta
18	chr3:121381600-121402400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:121381600-121402400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:121381600-121402600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr3:121381600-121402800	Strong transcription	Liver	Liver
22	chr3:121381800-121396600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:121381800-121401200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:121381800-121402600	Strong transcription	Primary T cells from cord blood	blood
25	chr3:121382000-121401800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:121382200-121401600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:121382400-121401800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:121382600-121396800	Strong transcription	Adipose Nuclei	Adipose
29	chr3:121382600-121399400	Strong transcription	Left Ventricle	heart
30	chr3:121382600-121401600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:121382800-121402600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:121383000-121400200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:121384000-121395400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:121384200-121399200	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:121384200-121402600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:121385600-121394800	Weak transcription	Colonic Mucosa	Colon
37	chr3:121385600-121398400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:121385800-121395200	Weak transcription	Fetal Brain Male	brain
39	chr3:121386000-121395400	Weak transcription	K562	blood
40	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:121386800-121395000	Weak transcription	Small Intestine	intestine
42	chr3:121387000-121394800	Weak transcription	Right Ventricle	heart
43	chr3:121387000-121395200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:121388200-121394800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:121388200-121395000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:121388200-121395200	Weak transcription	NHEK	skin
47	chr3:121388400-121394800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:121388400-121394800	Weak transcription	Gastric	stomach
49	chr3:121388400-121395000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:121388400-121395000	Weak transcription	Spleen	Spleen

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