Variant report

Variant	rs59361541
Chromosome Location	chr3:194869939-194869940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:194868265-194872140	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:194868269-194872203	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:194868355-194872209	HUVEC	blood vessel:	n/a	n/a
4	CHD1	chr3:194868421-194871809	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:194868262-194872259	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:194869898-194871874	HUVEC	blood vessel:	n/a	n/a
7	GATA3	chr3:194869779-194870371	SK-N-SH	brain:	n/a	chr3:194870039-194870055 chr3:194870336-194870346
8	POLR2A	chr3:194869919-194871774	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:194869872-194872144	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:194868342-194871929	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:194868149-194872233	HUVEC	blood vessel:	n/a	n/a
12	MTA3	chr3:194868157-194872051	GM12878	blood:	n/a	n/a
13	GATA2	chr3:194869873-194870780	SH-SY5Y	brain:	n/a	chr3:194870039-194870055 chr3:194870529-194870546 chr3:194870336-194870346 chr3:194870540-194870547 chr3:194870533-194870554 chr3:194870540-194870547 chr3:194870540-194870547
14	GATA3	chr3:194869890-194870394	SK-N-SH	brain:	n/a	chr3:194870039-194870055 chr3:194870336-194870346
15	GATA3	chr3:194869425-194870681	SH-SY5Y	brain:	n/a	chr3:194870039-194870055 chr3:194870529-194870546 chr3:194870336-194870346 chr3:194870540-194870547 chr3:194870533-194870554 chr3:194870540-194870547 chr3:194870540-194870547
16	POLR2A	chr3:194868848-194870192	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194869726..194872527-chr3:194883949..194885510,2	K562	blood:
2	chr3:194868967..194870771-chr3:194979716..194982181,2	K562	blood:

Variant related genes	Relation type
RN7SL36P	TF binding region
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11707112	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710992	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1874100	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1874104	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2279633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58948928	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59910866	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60922537	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62285217	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62285221	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285224	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62285225	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62285226	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62285227	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62285228	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62285231	0.94[ASN][1000 genomes]
rs62290329	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62290330	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62290331	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62290344	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62290347	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62290351	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62290352	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62290354	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7616009	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873120	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs952586	0.84[AMR][1000 genomes];0.88[EUR][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	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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
2	chr3:194854600-194871000	Weak transcription	Fetal Brain Female	brain
3	chr3:194860800-194870200	Weak transcription	Right Ventricle	heart
4	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
5	chr3:194861200-194872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:194861600-194870800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:194861800-194870800	Weak transcription	Aorta	Aorta
8	chr3:194861800-194871000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:194861800-194871200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:194861800-194872800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:194861800-194875000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:194862400-194870600	Weak transcription	Osteobl	bone
13	chr3:194862400-194897800	Weak transcription	Dnd41	blood
14	chr3:194863800-194870200	Weak transcription	Ovary	ovary
15	chr3:194864400-194870800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:194865000-194871000	Enhancers	Fetal Thymus	thymus
17	chr3:194866600-194870200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:194866800-194870600	Enhancers	K562	blood
19	chr3:194867200-194871800	Enhancers	Spleen	Spleen
20	chr3:194867400-194870000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:194867400-194871000	Weak transcription	Brain Substantia Nigra	brain
22	chr3:194867600-194871000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:194867800-194870000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:194867800-194872000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:194867800-194872400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:194868000-194870000	Active TSS	GM12878-XiMat	blood
27	chr3:194868000-194870400	Active TSS	Rectal Smooth Muscle	rectum
28	chr3:194868000-194870800	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:194868200-194870200	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:194868200-194871000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:194868200-194871400	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr3:194868200-194871800	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:194868200-194872000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:194868200-194872200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr3:194868200-194872200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:194868200-194877800	Enhancers	Fetal Stomach	stomach
37	chr3:194868400-194870800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:194868400-194870800	Enhancers	Fetal Lung	lung
39	chr3:194868400-194871000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr3:194868400-194871000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr3:194868400-194871000	Flanking Active TSS	HUVEC	blood vessel
42	chr3:194868400-194872000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:194868400-194877400	Enhancers	Fetal Heart	heart
44	chr3:194868600-194870800	Weak transcription	Brain Anterior Caudate	brain
45	chr3:194868600-194871000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:194868600-194871000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr3:194868600-194871800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:194868800-194870200	Weak transcription	Esophagus	oesophagus
49	chr3:194868800-194870200	Weak transcription	Lung	lung
50	chr3:194868800-194870600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links