Variant report

Variant	rs7909988
Chromosome Location	chr10:5736388-5736389
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5733731..5736743-chr10:5750015..5755601,4	MCF-7	breast:
2	chr10:5487726..5489985-chr10:5734513..5736734,2	K562	blood:
3	chr10:5724274..5728540-chr10:5734829..5741563,8	MCF-7	breast:
4	chr10:5735790..5738712-chr10:5931841..5933412,2	MCF-7	breast:
5	chr10:5734808..5736462-chr10:5936256..5938867,2	K562	blood:
6	chr10:5702075..5704019-chr10:5735223..5736822,2	MCF-7	breast:
7	chr10:5487726..5489985-chr10:5734513..5736734,3	K562	blood:
8	chr10:5733787..5736575-chr10:5751182..5753712,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173848	Chromatin interaction
ENSG00000108021	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000134452	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10737012	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10737013	0.90[EUR][1000 genomes]
rs10737019	0.87[EUR][1000 genomes]
rs10752069	0.88[EUR][1000 genomes]
rs10752110	0.81[EUR][1000 genomes]
rs10795347	0.84[EUR][1000 genomes]
rs10795485	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10795488	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10795510	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10795515	0.86[EUR][1000 genomes]
rs10795520	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs10795541	0.84[CEU][hapmap]
rs10905065	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs10905137	0.82[EUR][1000 genomes]
rs11254266	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11255228	0.80[EUR][1000 genomes]
rs11598374	0.82[ASN][1000 genomes]
rs12571639	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1317420	0.88[EUR][1000 genomes]
rs1567706	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1567707	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1858447	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2175630	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2244755	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2380199	0.89[CEU][hapmap]
rs2380202	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2497	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2797488	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2890365	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs2892078	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736462	0.82[EUR][1000 genomes]
rs4237365	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4748307	0.80[EUR][1000 genomes]
rs4748913	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4748916	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60840965	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61832743	0.80[EUR][1000 genomes]
rs6602240	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7071811	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7078711	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089100	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7096742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100576	0.88[EUR][1000 genomes]
rs7896749	0.88[EUR][1000 genomes]
rs7906719	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7913067	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9423726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9423930	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9423948	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv8600	chr10:5733691-5736727	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7909988	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs7909988	GDI2	cis	uninvolved skin	skin_eQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5728800-5746800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr10:5734800-5763400	Weak transcription	HSMM	muscle
3	chr10:5735000-5736400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:5735000-5736800	Enhancers	Small Intestine	intestine
5	chr10:5735200-5736400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:5735200-5736400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr10:5735200-5736400	Enhancers	Duodenum Mucosa	Duodenum
8	chr10:5735200-5736400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr10:5735200-5736400	Enhancers	Fetal Thymus	thymus
10	chr10:5735200-5736600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:5735200-5736600	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr10:5735200-5736800	Enhancers	Primary B cells from peripheral blood	blood
13	chr10:5735200-5736800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr10:5735200-5736800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr10:5735200-5736800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr10:5735200-5737000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr10:5735200-5737000	Enhancers	Brain Substantia Nigra	brain
18	chr10:5735200-5737200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr10:5735200-5737400	Enhancers	Primary B cells from cord blood	blood
20	chr10:5735200-5737600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr10:5735200-5737600	Weak transcription	Dnd41	blood
22	chr10:5735200-5737800	Weak transcription	Psoas Muscle	Psoas
23	chr10:5735200-5738800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr10:5735200-5739000	Weak transcription	Fetal Intestine Large	intestine
25	chr10:5735200-5739400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:5735200-5739400	Weak transcription	Lung	lung
27	chr10:5735200-5739400	Weak transcription	Pancreas	Pancrea
28	chr10:5735200-5739800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr10:5735200-5743000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr10:5735200-5749000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:5735200-5750600	Weak transcription	Gastric	stomach
32	chr10:5735200-5767000	Weak transcription	Fetal Muscle Leg	muscle
33	chr10:5735400-5736400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr10:5735400-5736400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr10:5735400-5736400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr10:5735400-5736600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr10:5735400-5736600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr10:5735400-5736600	Enhancers	Brain Cingulate Gyrus	brain
39	chr10:5735400-5736600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr10:5735400-5737000	Enhancers	Primary hematopoietic stem cells	blood
41	chr10:5735400-5737000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr10:5735400-5737000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr10:5735400-5737000	Enhancers	Brain Hippocampus Middle	brain
44	chr10:5735400-5737200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr10:5735400-5737400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:5735400-5737800	Weak transcription	Left Ventricle	heart
47	chr10:5735400-5738000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr10:5735400-5738000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr10:5735400-5738200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr10:5735400-5738200	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links