Variant report

Variant	rs6602240
Chromosome Location	chr10:5816751-5816752
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:5816210-5816780	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:5816507-5816917	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5815489..5817039-chr10:5930914..5932543,2	MCF-7	breast:
2	chr10:5814904..5817152-chr10:5861494..5864135,2	K562	blood:
3	chr10:5816487..5819223-chr10:5854186..5856565,2	MCF-7	breast:
4	chr10:5815026..5819070-chr10:5852954..5857275,5	MCF-7	breast:
5	chr10:5707689..5709462-chr10:5814945..5817598,2	MCF-7	breast:

No data

Variant related genes	Relation type
NRBF2P5	TF binding region
ENSG00000196372	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000272764	Chromatin interaction
ENSG00000057608	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10737012	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10737019	0.81[EUR][1000 genomes]
rs10737021	0.84[EUR][1000 genomes]
rs10752110	0.88[EUR][1000 genomes]
rs10752111	0.84[EUR][1000 genomes]
rs10795347	0.83[CEU][hapmap]
rs10795485	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10795488	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10795510	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10795520	0.80[EUR][1000 genomes]
rs10795541	0.96[CEU][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs10795547	0.84[EUR][1000 genomes]
rs10905065	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs10905137	0.87[EUR][1000 genomes]
rs11254266	0.82[CHB][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs11255085	0.86[EUR][1000 genomes]
rs11255228	0.87[EUR][1000 genomes]
rs11598374	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12571639	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1317420	0.80[EUR][1000 genomes]
rs1567706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1567707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1858447	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2175630	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2244755	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2380199	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2380202	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2380203	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2497	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2797488	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2890365	0.96[CEU][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs2892078	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736462	0.87[EUR][1000 genomes]
rs4237365	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748913	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4748916	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60840965	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6602259	0.82[EUR][1000 genomes]
rs6602278	0.90[TSI][hapmap]
rs7071811	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7078711	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7089100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7096742	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7100576	0.81[EUR][1000 genomes]
rs7896749	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7906719	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7909988	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]
rs7913067	0.88[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs7916827	0.81[EUR][1000 genomes]
rs9423726	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9423930	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6602240	GDI2	cis	uninvolved skin	skin_eQTL
rs6602240	GDI2	cis	cerebellum	SCAN
rs6602240	GDI2	cis	parietal	SCAN
rs6602240	GDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5762600-5843400	Strong transcription	Dnd41	blood
2	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:5781400-5818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:5784800-5818000	Weak transcription	Stomach Mucosa	stomach
6	chr10:5788000-5818000	Strong transcription	Duodenum Mucosa	Duodenum
7	chr10:5795000-5817800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:5796000-5822400	Strong transcription	Fetal Intestine Large	intestine
9	chr10:5797200-5819000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr10:5797400-5816800	Strong transcription	Fetal Thymus	thymus
11	chr10:5797400-5847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr10:5797600-5817200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:5797600-5817800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:5797600-5817800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr10:5798000-5817000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr10:5798000-5817600	Strong transcription	Primary B cells from cord blood	blood
17	chr10:5798000-5818200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr10:5798000-5842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr10:5798200-5817000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr10:5798200-5843000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr10:5798400-5817800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:5798400-5817800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:5798600-5817000	Strong transcription	Placenta	Placenta
24	chr10:5798600-5817400	Strong transcription	Osteobl	bone
25	chr10:5798600-5817800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr10:5798600-5818400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:5798600-5820200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:5798600-5842800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr10:5798800-5817800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:5804800-5818200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:5805000-5843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:5805200-5819000	Strong transcription	GM12878-XiMat	blood
33	chr10:5805600-5818200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr10:5805800-5817600	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr10:5806000-5818200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr10:5806200-5817800	Strong transcription	Fetal Muscle Leg	muscle
37	chr10:5807400-5821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr10:5808400-5817800	Strong transcription	Liver	Liver
39	chr10:5808400-5826400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:5808600-5817800	Weak transcription	Psoas Muscle	Psoas
41	chr10:5808800-5817800	Weak transcription	Fetal Brain Male	brain
42	chr10:5808800-5825800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr10:5809000-5824400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr10:5810200-5817800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr10:5810400-5817800	Weak transcription	Aorta	Aorta
46	chr10:5810400-5818000	Weak transcription	Brain Angular Gyrus	brain
47	chr10:5810400-5818000	Weak transcription	Brain Anterior Caudate	brain
48	chr10:5810400-5824800	Weak transcription	Ovary	ovary
49	chr10:5810600-5817000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr10:5810800-5817800	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links