Variant report

Variant	rs2222826
Chromosome Location	chr3:121540609-121540610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121540007..121542032-chr3:121549979..121552263,2	K562	blood:
2	chr3:121539069..121540622-chr3:121552638..121555253,2	MCF-7	breast:
3	chr3:121537857..121540705-chr3:121553150..121557600,4	K562	blood:

Variant related genes	Relation type
ENSG00000145088	Chromatin interaction
ENSG00000173226	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10470411	0.87[EUR][1000 genomes]
rs10470412	0.87[EUR][1000 genomes]
rs10511407	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10934561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713268	0.87[EUR][1000 genomes]
rs12486309	0.87[EUR][1000 genomes]
rs12486310	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487516	0.87[EUR][1000 genomes]
rs12488692	0.87[EUR][1000 genomes]
rs12488717	0.81[AFR][1000 genomes]
rs12489110	0.81[AFR][1000 genomes]
rs12489142	0.86[EUR][1000 genomes]
rs12489686	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491109	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493270	0.87[EUR][1000 genomes]
rs12494523	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12629720	0.87[EUR][1000 genomes]
rs12634458	0.86[EUR][1000 genomes]
rs12695417	0.87[EUR][1000 genomes]
rs13100245	0.87[EUR][1000 genomes]
rs13321798	0.87[EUR][1000 genomes]
rs1881997	0.86[EUR][1000 genomes]
rs1881998	0.84[EUR][1000 genomes]
rs1920307	0.87[EUR][1000 genomes]
rs2689274	0.87[EUR][1000 genomes]
rs2689278	0.87[EUR][1000 genomes]
rs2689279	0.87[EUR][1000 genomes]
rs2689280	0.82[EUR][1000 genomes]
rs2689286	0.87[EUR][1000 genomes]
rs2700412	0.87[EUR][1000 genomes]
rs2700413	0.87[EUR][1000 genomes]
rs2700414	0.87[EUR][1000 genomes]
rs2700419	0.87[EUR][1000 genomes]
rs28844130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35354585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35692621	0.87[EUR][1000 genomes]
rs35723704	0.84[EUR][1000 genomes]
rs3805125	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805129	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805132	0.86[EUR][1000 genomes]
rs4048630	0.87[EUR][1000 genomes]
rs41271407	0.81[AFR][1000 genomes]
rs41271411	0.87[EUR][1000 genomes]
rs4603998	0.87[EUR][1000 genomes]
rs4610269	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4676760	0.87[EUR][1000 genomes]
rs4676761	0.87[EUR][1000 genomes]
rs4676762	0.83[EUR][1000 genomes]
rs57365001	0.87[EUR][1000 genomes]
rs58485759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59064186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59228534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61567016	0.87[EUR][1000 genomes]
rs6438681	0.87[EUR][1000 genomes]
rs72959293	0.87[EUR][1000 genomes]
rs72961314	0.87[EUR][1000 genomes]
rs7619918	0.87[EUR][1000 genomes]
rs7620562	0.87[EUR][1000 genomes]
rs7625960	0.87[EUR][1000 genomes]
rs7626052	0.87[EUR][1000 genomes]
rs7627291	0.87[EUR][1000 genomes]
rs7647585	0.87[EUR][1000 genomes]
rs7650341	0.87[EUR][1000 genomes]
rs9818733	0.87[EUR][1000 genomes]
rs9831798	0.86[EUR][1000 genomes]
rs9832735	0.86[EUR][1000 genomes]
rs9834185	0.87[EUR][1000 genomes]
rs9865926	0.87[EUR][1000 genomes]
rs9869891	0.87[EUR][1000 genomes]
rs9877671	0.87[EUR][1000 genomes]
rs9882841	0.83[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	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	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
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2222826	HCLS1	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121491600-121552600	Weak transcription	NHLF	lung
2	chr3:121494200-121544200	Weak transcription	Fetal Brain Male	brain
3	chr3:121500200-121541400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:121507000-121545400	Weak transcription	Fetal Heart	heart
5	chr3:121508600-121541400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:121524800-121541400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:121526000-121542800	Weak transcription	NH-A	brain
8	chr3:121528000-121553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:121530800-121541200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:121530800-121543200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:121530800-121552200	Weak transcription	Small Intestine	intestine
12	chr3:121530800-121552400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:121530800-121552800	Weak transcription	HSMMtube	muscle
14	chr3:121530800-121553000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:121530800-121553200	Weak transcription	Esophagus	oesophagus
16	chr3:121531000-121540800	Weak transcription	Aorta	Aorta
17	chr3:121531000-121542800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:121531000-121543000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:121531000-121552800	Weak transcription	Fetal Stomach	stomach
20	chr3:121531000-121552800	Weak transcription	Pancreas	Pancrea
21	chr3:121531000-121552800	Weak transcription	Right Ventricle	heart
22	chr3:121531000-121552800	Weak transcription	Spleen	Spleen
23	chr3:121531200-121549600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:121534200-121544600	Weak transcription	Brain Substantia Nigra	brain
25	chr3:121534400-121542000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:121535000-121541400	Strong transcription	Primary B cells from cord blood	blood
27	chr3:121535400-121542000	Strong transcription	Fetal Intestine Large	intestine
28	chr3:121535400-121551200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:121535600-121541600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:121535600-121542200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:121535600-121545200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:121535800-121541600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:121536000-121542000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:121536000-121551600	Strong transcription	Fetal Thymus	thymus
35	chr3:121536200-121541200	Weak transcription	Psoas Muscle	Psoas
36	chr3:121536200-121541200	Strong transcription	NHEK	skin
37	chr3:121536200-121552800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:121536400-121548000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:121536600-121542000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:121536800-121540800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:121536800-121541600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:121536800-121543800	Weak transcription	Ovary	ovary
43	chr3:121537000-121540800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:121537000-121540800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:121537000-121541400	Weak transcription	Fetal Intestine Small	intestine
46	chr3:121537000-121541800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:121537000-121541800	Strong transcription	Dnd41	blood
48	chr3:121537000-121543000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:121537000-121544400	Weak transcription	Colonic Mucosa	Colon
50	chr3:121537200-121540800	Weak transcription	Fetal Kidney	kidney

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