Variant report

Variant	rs2355323
Chromosome Location	chr3:50631800-50631801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50619029..50623920-chr3:50628439..50631863,6	MCF-7	breast:
2	chr3:50630568..50632626-chr3:51424931..51427398,2	MCF-7	breast:
3	chr3:50625968..50628084-chr3:50630871..50632598,2	K562	blood:
4	chr3:50614741..50617207-chr3:50631389..50633119,2	MCF-7	breast:
5	chr3:50605337..50613345-chr3:50630313..50633692,8	MCF-7	breast:
6	chr3:50631688..50633387-chr3:50649479..50651263,2	K562	blood:
7	chr3:50626963..50632967-chr3:50633102..50640850,17	K562	blood:
8	chr3:50311886..50314676-chr3:50630093..50632260,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000114735	Chromatin interaction
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1013233	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1034405	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs11130252	0.84[EUR][1000 genomes]
rs11712367	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11716398	0.87[AMR][1000 genomes]
rs11719998	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491425	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493985	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12639126	0.81[CEU][hapmap]
rs129310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13076850	0.89[EUR][1000 genomes]
rs13083004	0.89[EUR][1000 genomes]
rs13084476	0.84[EUR][1000 genomes]
rs13091933	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1385025	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs175634	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17787569	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1824281	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs1971976	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs201193	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201194	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs201196	0.91[EUR][1000 genomes]
rs201197	0.80[EUR][1000 genomes]
rs201198	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2227280	0.90[EUR][1000 genomes]
rs2232248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232253	0.90[EUR][1000 genomes]
rs2269505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269507	0.90[EUR][1000 genomes]
rs2355321	0.90[EUR][1000 genomes]
rs2675773	0.88[CEU][hapmap]
rs2675816	0.83[CEU][hapmap]
rs34202063	0.90[EUR][1000 genomes]
rs34267788	0.81[EUR][1000 genomes]
rs34399912	0.90[EUR][1000 genomes]
rs34434811	0.81[EUR][1000 genomes]
rs34584636	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs34756253	0.84[EUR][1000 genomes]
rs34848480	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34889917	0.90[EUR][1000 genomes]
rs35655236	0.89[EUR][1000 genomes]
rs35690191	0.89[EUR][1000 genomes]
rs35714264	0.85[EUR][1000 genomes]
rs35864641	0.81[EUR][1000 genomes]
rs375544	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3792325	0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3792328	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3804627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804632	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs388483	0.93[YRI][hapmap]
rs391620	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3943212	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs396302	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs398703	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs399484	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs399971	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414171	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs417592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs441516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443030	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs443436	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs448028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4485709	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4533647	0.81[EUR][1000 genomes]
rs453570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688712	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs490634	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs59949730	0.90[EUR][1000 genomes]
rs616589	0.91[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs622502	0.81[EUR][1000 genomes]
rs628081	0.94[CEU][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446212	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6446213	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs6446220	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs67588094	0.90[EUR][1000 genomes]
rs6778680	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs6779819	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes]
rs67813889	0.92[EUR][1000 genomes]
rs6784166	0.85[EUR][1000 genomes]
rs6787521	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6796769	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs695170	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71326937	0.90[EUR][1000 genomes]
rs728901	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs750453	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs750510	0.89[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs751851	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs754298	0.82[EUR][1000 genomes]
rs7615703	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7635666	0.87[AMR][1000 genomes]
rs7645212	0.80[AMR][1000 genomes]
rs7646236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808149	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs809451	0.81[EUR][1000 genomes]
rs809454	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs813243	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs900735	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9682401	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9825535	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9826757	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9830920	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2355323	HEMK1	cis	Lymphoblastoid	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
2	chr3:50623000-50636600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:50623200-50633800	Enhancers	Fetal Thymus	thymus
4	chr3:50626800-50632400	Enhancers	Liver	Liver
5	chr3:50628200-50632400	Enhancers	Fetal Heart	heart
6	chr3:50628400-50632000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:50628400-50633800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:50628600-50633600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:50628600-50635600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:50628600-50638200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:50628800-50632200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:50628800-50632400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:50628800-50633600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:50628800-50633800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:50628800-50634000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:50628800-50637200	Weak transcription	A549	lung
17	chr3:50628800-50637400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:50629000-50631800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:50629000-50632000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr3:50629000-50633200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:50629000-50634000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr3:50629000-50634000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:50629000-50637600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:50629800-50635600	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:50630200-50632200	Enhancers	HepG2	liver
26	chr3:50630400-50636600	Weak transcription	Ovary	ovary
27	chr3:50630400-50637200	Weak transcription	NHDF-Ad	bronchial
28	chr3:50630600-50635600	Weak transcription	Fetal Lung	lung
29	chr3:50630600-50636600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:50630600-50636800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:50630600-50637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:50630600-50637400	Weak transcription	Stomach Mucosa	stomach
33	chr3:50630800-50631800	Weak transcription	Pancreas	Pancrea
34	chr3:50630800-50631800	Weak transcription	Psoas Muscle	Psoas
35	chr3:50630800-50631800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:50630800-50631800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:50630800-50633400	Weak transcription	K562	blood
38	chr3:50630800-50634800	Enhancers	Dnd41	blood
39	chr3:50630800-50636000	Weak transcription	Esophagus	oesophagus
40	chr3:50630800-50636000	Weak transcription	Right Ventricle	heart
41	chr3:50630800-50636200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:50630800-50636400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:50630800-50636400	Weak transcription	Fetal Stomach	stomach
44	chr3:50630800-50636600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:50630800-50636800	Weak transcription	Gastric	stomach
46	chr3:50630800-50637000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:50631000-50633000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:50631000-50636600	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:50631000-50637000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:50631200-50632200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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