Variant report

Variant	rs1873645
Chromosome Location	chr3:121348499-121348500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12489511	0.92[CHB][hapmap]
rs12631824	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13067629	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1492177	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1574655	0.90[EUR][1000 genomes]
rs1574735	0.90[EUR][1000 genomes]
rs1919552	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs1919557	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs1986874	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2001390	0.90[EUR][1000 genomes]
rs2001391	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs2070179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2840143	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35295338	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772127	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4478028	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4676684	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4676685	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4676686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438645	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438660	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs6770719	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs6791896	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792659	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794341	0.90[EUR][1000 genomes]
rs6794677	0.87[EUR][1000 genomes]
rs6802033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6803839	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]
rs6807711	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7375038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429247	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7430165	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7611913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620842	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7646585	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];0.92[EUR][1000 genomes]
rs9289172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9681209	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs9809114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9812411	0.90[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes]
rs9829053	0.88[EUR][1000 genomes]
rs9832267	0.92[EUR][1000 genomes]
rs9835182	0.90[EUR][1000 genomes]
rs9854052	0.92[EUR][1000 genomes]
rs9861992	0.92[EUR][1000 genomes]
rs9864907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9876021	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic 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	15 gene(s)	inside rSNPs	diseases
6	nsv999349	chr3:121253990-121360206	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1873645	HCLS1	cis	multi-tissue	Pritchard
rs1873645	HCLS1	Cis_1M	lymphoblastoid	RTeQTL
rs1873645	HCLS1	cis	Lymphoblastoid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121342000-121350000	Weak transcription	Liver	Liver
2	chr3:121343800-121353000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:121345000-121349400	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:121345600-121349600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:121345600-121376800	Weak transcription	Esophagus	oesophagus
6	chr3:121345800-121348600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:121345800-121350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:121346000-121348800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:121346200-121350000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:121346200-121351600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:121346400-121349000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:121346400-121349800	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:121346400-121351800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:121346400-121353200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:121346800-121351800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:121347000-121349200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:121347000-121349200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:121347000-121378000	Weak transcription	Right Ventricle	heart
19	chr3:121347200-121348800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:121347200-121349400	Enhancers	Fetal Heart	heart
21	chr3:121347200-121352600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:121347200-121364400	Strong transcription	Primary B cells from cord blood	blood
23	chr3:121347400-121349000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:121347400-121349000	Weak transcription	Dnd41	blood
25	chr3:121347400-121349600	Weak transcription	Thymus	Thymus
26	chr3:121347400-121349800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:121347400-121350800	Weak transcription	Right Atrium	heart
28	chr3:121347400-121352200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:121347400-121367200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:121347600-121350200	Weak transcription	HUVEC	blood vessel
31	chr3:121347600-121353000	Strong transcription	Fetal Thymus	thymus
32	chr3:121347600-121359400	Strong transcription	Primary T cells from cord blood	blood
33	chr3:121347600-121364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:121347600-121364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:121347600-121364600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:121347800-121349400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:121347800-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:121348000-121364600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:121348000-121364600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
41	chr3:121348200-121364600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:121348400-121348600	Enhancers	Psoas Muscle	Psoas
43	chr3:121348400-121348800	Genic enhancers	Left Ventricle	heart
44	chr3:121348400-121348800	Strong transcription	GM12878-XiMat	blood
45	chr3:121348400-121357400	Strong transcription	Spleen	Spleen
46	chr3:121348400-121364600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:121348400-121364600	Strong transcription	Monocytes-CD14+_RO01746	blood

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