Variant report

Variant	rs55993159
Chromosome Location	chr3:194830035-194830036
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194827712..194831083-chr3:194838703..194842904,3	K562	blood:
2	chr3:194827345..194830265-chr3:194841540..194843124,2	K562	blood:
3	chr3:194828404..194831478-chr3:194832596..194835567,3	K562	blood:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1494327	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28744613	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4079351	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4677657	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677658	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677659	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677660	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677804	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677808	0.92[AFR][1000 genomes]
rs4677809	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55980698	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268394	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437456	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6437457	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67660032	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623657	0.95[ASN][1000 genomes]
rs869520	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903301	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903302	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903307	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9757797	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9859891	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9872141	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9875441	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882947	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv963494	chr3:194826599-194833987	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv3339583	chr3:194828063-194833661	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv3338798	chr3:194829713-194832111	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194815800-194830200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:194817200-194831200	Weak transcription	Gastric	stomach
3	chr3:194822000-194846600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:194823600-194831200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:194823800-194833200	Weak transcription	HSMM	muscle
6	chr3:194824000-194831000	Weak transcription	HSMMtube	muscle
7	chr3:194824000-194838800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:194825400-194830200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:194825400-194830400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:194825800-194838400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:194826600-194835800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:194826800-194838600	Weak transcription	Hela-S3	cervix
13	chr3:194827200-194830200	Weak transcription	NHLF	lung
14	chr3:194827200-194831200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:194827200-194831200	Weak transcription	Lung	lung
16	chr3:194827200-194831800	Weak transcription	GM12878-XiMat	blood
17	chr3:194827200-194838800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:194827200-194838800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:194827400-194830400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:194827400-194831200	Weak transcription	Esophagus	oesophagus
21	chr3:194827400-194833400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:194827400-194838400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:194827400-194853600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:194827400-194861200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:194827600-194830200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:194827600-194830200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:194827600-194830200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:194827600-194830200	Weak transcription	Dnd41	blood
29	chr3:194827600-194830800	Weak transcription	Right Ventricle	heart
30	chr3:194827600-194830800	Weak transcription	NHEK	skin
31	chr3:194827600-194831000	Weak transcription	Thymus	Thymus
32	chr3:194827600-194831200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:194827600-194831200	Weak transcription	Pancreas	Pancrea
34	chr3:194827600-194831200	Weak transcription	Right Atrium	heart
35	chr3:194827600-194831200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:194827600-194831200	Weak transcription	Spleen	Spleen
37	chr3:194827600-194831400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:194827600-194831800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:194827600-194833400	Weak transcription	Ovary	ovary
40	chr3:194827600-194834000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:194827600-194834400	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:194827600-194838000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:194827600-194838000	Weak transcription	NH-A	brain
44	chr3:194827600-194838600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:194827600-194838600	Weak transcription	Stomach Mucosa	stomach
46	chr3:194827600-194839200	Weak transcription	Psoas Muscle	Psoas
47	chr3:194827600-194840000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:194827600-194840200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:194827600-194840800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:194827600-194841200	Weak transcription	Brain Anterior Caudate	brain

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