Variant report

Variant	rs6803839
Chromosome Location	chr3:121397997-121397998
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12489511	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12490565	0.95[CEU][hapmap];0.92[CHB][hapmap]
rs12631824	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1492177	0.95[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes]
rs1574655	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1574735	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873645	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1919552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1919557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986351	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1986874	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001390	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070179	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2840143	0.95[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes]
rs35295338	0.87[EUR][1000 genomes]
rs3772127	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4478028	0.82[EUR][1000 genomes]
rs4676684	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4676685	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4676686	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4676751	0.80[EUR][1000 genomes]
rs6438645	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6438660	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs6770719	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6776703	0.80[EUR][1000 genomes]
rs6791896	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792659	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794341	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6794677	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6802033	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6807711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7375038	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7429247	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7430165	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611913	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7620842	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7646346	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs7646585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289172	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289173	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9681209	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs9809114	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812411	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9829053	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9832267	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835182	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9854052	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9861992	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864907	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876021	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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
rs6803839	HCLS1	Cis_1M	lymphoblastoid	RTeQTL
rs6803839	HCLS1	cis	Lymphoblastoid	GTEx
rs6803839	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	chr3:121380400-121402400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:121380400-121402800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:121380400-121406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:121380600-121413800	Weak transcription	Stomach Mucosa	stomach
7	chr3:121381000-121401800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:121381000-121403200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:121381400-121406800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr3:121381600-121401600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:121381600-121402200	Strong transcription	Placenta	Placenta
12	chr3:121381600-121402400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr3:121381600-121402400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:121381600-121402600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr3:121381600-121402800	Strong transcription	Liver	Liver
16	chr3:121381800-121401200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:121381800-121402600	Strong transcription	Primary T cells from cord blood	blood
18	chr3:121382000-121401800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:121382200-121401600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:121382400-121401800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:121382600-121399400	Strong transcription	Left Ventricle	heart
22	chr3:121382600-121401600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:121382800-121402600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:121383000-121400200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:121384200-121399200	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:121384200-121402600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:121385600-121398400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:121390200-121402000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:121390200-121402400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:121390400-121402400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:121390800-121403400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:121391200-121400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:121391400-121400200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:121391800-121402600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:121392000-121398400	Weak transcription	Fetal Heart	heart
37	chr3:121392400-121399000	Strong transcription	Lung	lung
38	chr3:121392400-121401200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:121392800-121401400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:121392800-121401600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:121392800-121401600	Strong transcription	Primary B cells from cord blood	blood
42	chr3:121392800-121401800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:121393000-121398000	Weak transcription	Fetal Intestine Small	intestine
44	chr3:121393000-121401800	Strong transcription	HSMM	muscle
45	chr3:121393400-121401800	Strong transcription	GM12878-XiMat	blood
46	chr3:121394200-121399600	Strong transcription	Hela-S3	cervix
47	chr3:121394200-121400800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:121394600-121402200	Strong transcription	HSMMtube	muscle
49	chr3:121395600-121398800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:121396000-121398200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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