Variant report

Variant	rs62285228
Chromosome Location	chr3:194880965-194880966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194879007..194881053-chr3:194979480..194982311,2	K562	blood:
2	chr3:194836997..194839918-chr3:194880679..194883112,2	K562	blood:
3	chr3:194879313..194881021-chr3:194894855..194897283,2	MCF-7	breast:
4	chr3:194870262..194872274-chr3:194880520..194882642,2	K562	blood:
5	chr3:194879840..194881692-chr3:194900733..194902679,2	K562	blood:
6	chr3:194879677..194882151-chr3:194884432..194886543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11707112	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633566	0.83[AFR][1000 genomes]
rs1874100	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1874104	0.82[EUR][1000 genomes]
rs2279633	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57475252	0.80[AFR][1000 genomes]
rs58948928	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59361541	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59910866	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60922537	0.81[EUR][1000 genomes]
rs62285217	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62285221	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62285224	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285225	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62285231	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62290329	0.82[EUR][1000 genomes]
rs62290330	0.81[EUR][1000 genomes]
rs62290331	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62290344	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62290347	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62290351	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62290352	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62290354	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7616009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873120	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs952586	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
17	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases
20	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
2	chr3:194862400-194897800	Weak transcription	Dnd41	blood
3	chr3:194868800-194885400	Enhancers	Fetal Muscle Leg	muscle
4	chr3:194871400-194887400	Enhancers	Primary hematopoietic stem cells	blood
5	chr3:194871600-194881200	Weak transcription	Liver	Liver
6	chr3:194871800-194882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:194872000-194882800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:194872000-194883000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:194872000-194883000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:194873000-194884400	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:194873000-194884600	Enhancers	Fetal Thymus	thymus
12	chr3:194874000-194889800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:194876200-194881000	Enhancers	HepG2	liver
14	chr3:194876400-194881200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:194876600-194881000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:194876600-194893000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:194876800-194881400	Weak transcription	Esophagus	oesophagus
18	chr3:194876800-194893800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:194877000-194881000	Weak transcription	NHEK	skin
20	chr3:194877000-194881400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:194877000-194881400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:194877200-194881200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:194877200-194881200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:194877200-194881200	Weak transcription	Stomach Mucosa	stomach
25	chr3:194877200-194884200	Weak transcription	Gastric	stomach
26	chr3:194877200-194891200	Weak transcription	Psoas Muscle	Psoas
27	chr3:194877400-194881200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:194877400-194881400	Weak transcription	Pancreas	Pancrea
29	chr3:194877400-194883000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:194877400-194888600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:194877400-194888800	Weak transcription	Brain Germinal Matrix	brain
32	chr3:194877600-194881000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:194877600-194881200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:194877800-194881400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:194877800-194881800	Enhancers	Fetal Intestine Small	intestine
36	chr3:194877800-194882800	Weak transcription	Brain Angular Gyrus	brain
37	chr3:194877800-194883000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:194878000-194882200	Enhancers	Fetal Intestine Large	intestine
39	chr3:194878200-194882200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:194878200-194882400	Enhancers	Fetal Heart	heart
41	chr3:194878200-194885200	Enhancers	Fetal Stomach	stomach
42	chr3:194878600-194881000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:194878600-194882600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:194878600-194883000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:194879000-194881000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:194879000-194883000	Weak transcription	Thymus	Thymus
47	chr3:194879200-194881200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:194879600-194883400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:194880000-194881400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:194880000-194881600	Enhancers	Duodenum Smooth Muscle	Duodenum

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