Variant report

Variant	rs9289172
Chromosome Location	chr3:121356368-121356369
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121355706..121357313-chr3:121467523..121469117,2	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12489511	0.92[CHB][hapmap]
rs12490565	0.90[CEU][hapmap];0.84[CHB][hapmap]
rs12631824	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13067629	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1492177	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1574655	0.91[EUR][1000 genomes]
rs1574735	0.91[EUR][1000 genomes]
rs1873645	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]
rs1919552	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs1919557	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1986874	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2001390	0.91[EUR][1000 genomes]
rs2001391	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs2070179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2840143	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35295338	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3772127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478028	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676684	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4676685	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4676686	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438645	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438660	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs6770719	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs6791896	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792659	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6794341	0.91[EUR][1000 genomes]
rs6794677	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6802033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803839	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	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7375038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7429247	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7430165	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7611913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7620842	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646346	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs7646585	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9289173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812411	0.90[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9829053	0.89[EUR][1000 genomes]
rs9832267	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9835182	0.91[EUR][1000 genomes]
rs9854052	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9861992	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9864907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9876021	0.83[AMR][1000 genomes];0.92[EUR][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	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9289172	HCLS1	cis	multi-tissue	Pritchard
rs9289172	HCLS1	Cis_1M	lymphoblastoid	RTeQTL
rs9289172	HCLS1	cis	Lymphoblastoid	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121345600-121376800	Weak transcription	Esophagus	oesophagus
2	chr3:121347000-121378000	Weak transcription	Right Ventricle	heart
3	chr3:121347200-121364400	Strong transcription	Primary B cells from cord blood	blood
4	chr3:121347400-121367200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:121347600-121359400	Strong transcription	Primary T cells from cord blood	blood
6	chr3:121347600-121364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:121347600-121364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:121347600-121364600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:121347800-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:121348000-121364600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:121348000-121364600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
13	chr3:121348200-121364600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:121348400-121357400	Strong transcription	Spleen	Spleen
15	chr3:121348400-121364600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:121348400-121364600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:121348800-121358600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:121348800-121363000	Weak transcription	Left Ventricle	heart
19	chr3:121348800-121364400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:121348800-121367200	Weak transcription	Pancreas	Pancrea
21	chr3:121349000-121356600	Weak transcription	Brain Anterior Caudate	brain
22	chr3:121349000-121359000	Strong transcription	Primary hematopoietic stem cells	blood
23	chr3:121349000-121364600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:121349000-121364600	Strong transcription	Dnd41	blood
25	chr3:121349000-121378000	Weak transcription	Fetal Stomach	stomach
26	chr3:121349200-121359200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:121349200-121362000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:121349200-121364200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:121349400-121364600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:121349400-121367000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:121349600-121358600	Strong transcription	Thymus	Thymus
32	chr3:121349600-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:121349800-121359400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:121349800-121367000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:121350000-121357400	Strong transcription	Liver	Liver
36	chr3:121350000-121364600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:121350000-121364600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:121350200-121357400	Strong transcription	Placenta	Placenta
39	chr3:121350400-121357400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:121351000-121364600	Strong transcription	GM12878-XiMat	blood
41	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
42	chr3:121351400-121381400	Weak transcription	Gastric	stomach
43	chr3:121351600-121360800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:121351800-121358600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:121351800-121370400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:121352800-121357000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:121353400-121356600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:121353400-121364400	Strong transcription	Fetal Thymus	thymus
49	chr3:121353400-121376000	Weak transcription	Lung	lung
50	chr3:121354000-121381000	Weak transcription	Fetal Intestine Small	intestine

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