Variant report

Variant	rs55913768
Chromosome Location	chr10:5749449-5749450
allele	A/G
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	YY1	chr10:5749233-5749547	GM12892	blood:	n/a	chr10:5749388-5749400
2	YY1	chr10:5749279-5749511	K562	blood:	n/a	chr10:5749388-5749400
3	YY1	chr10:5749244-5749568	H1-hESC	embryonic stem cell:	n/a	chr10:5749388-5749400

No.	Distal block	Cell Line	Cell type
1	chr10:5748194..5752835-chr10:5754048..5756817,4	MCF-7	breast:
2	chr10:5739796..5741781-chr10:5749171..5751664,2	K562	blood:
3	chr10:5748219..5750363-chr10:5854486..5857836,3	K562	blood:
4	chr10:5726042..5728288-chr10:5749073..5750602,2	MCF-7	breast:
5	chr10:5749331..5751583-chr10:5752146..5753784,2	MCF-7	breast:
6	chr10:5725406..5728715-chr10:5747568..5751515,5	MCF-7	breast:

Variant related genes	Relation type
FAM208B	TF binding region
ENSG00000057608	Chromatin interaction
ENSG00000226647	Chromatin interaction
ENSG00000108021	Chromatin interaction
ENSG00000272764	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11254266	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282457	0.86[ASN][1000 genomes]
rs45575338	0.81[AFR][1000 genomes]
rs4748307	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748572	0.81[AFR][1000 genomes]
rs4750553	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61832743	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61832744	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72774056	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72774070	0.81[AFR][1000 genomes]
rs72774075	0.81[AFR][1000 genomes]
rs72774077	0.81[AFR][1000 genomes]
rs72774078	0.81[AFR][1000 genomes]
rs7910414	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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 target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv1796213	chr10:5716555-5766165	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv522415	chr10:5721653-5768493	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1050663	chr10:5737979-5785918	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv528504	chr10:5739054-5754611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55913768	GDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5734800-5763400	Weak transcription	HSMM	muscle
2	chr10:5735200-5750600	Weak transcription	Gastric	stomach
3	chr10:5735200-5767000	Weak transcription	Fetal Muscle Leg	muscle
4	chr10:5735400-5750800	Weak transcription	Spleen	Spleen
5	chr10:5735400-5761600	Weak transcription	NHEK	skin
6	chr10:5735400-5762000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:5735800-5752800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:5736200-5751600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:5736400-5753000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:5738600-5752400	Weak transcription	Primary B cells from cord blood	blood
11	chr10:5738600-5752800	Weak transcription	Right Atrium	heart
12	chr10:5738600-5769000	Weak transcription	Left Ventricle	heart
13	chr10:5739600-5752800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr10:5740200-5752000	Weak transcription	Stomach Mucosa	stomach
15	chr10:5740200-5752800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:5740400-5768600	Weak transcription	Psoas Muscle	Psoas
17	chr10:5741400-5760600	Weak transcription	Small Intestine	intestine
18	chr10:5741400-5765600	Weak transcription	A549	lung
19	chr10:5741600-5750200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr10:5741600-5753400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr10:5743200-5752400	Weak transcription	Brain Substantia Nigra	brain
22	chr10:5743200-5753600	Weak transcription	HepG2	liver
23	chr10:5743200-5762600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr10:5744200-5753000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr10:5745000-5750200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:5745000-5752000	Weak transcription	Liver	Liver
27	chr10:5746800-5752800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr10:5747200-5752000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:5747400-5749800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr10:5747400-5751600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:5748200-5749800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr10:5748200-5752400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr10:5748800-5751800	Weak transcription	Dnd41	blood
34	chr10:5749000-5749600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr10:5749000-5750000	Enhancers	K562	blood
36	chr10:5749000-5752800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr10:5749000-5753200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:5749200-5749600	Weak transcription	Primary T cells from cord blood	blood
39	chr10:5749200-5752000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr10:5749400-5749600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr10:5749400-5749600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr10:5749400-5750400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr10:5749400-5752800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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