Variant report

Variant	rs10025838
Chromosome Location	chr4:78120747-78120748
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78084268..78085795-chr4:78119137..78120989,2	K562	blood:
2	chr4:77991930..77994376-chr4:78120322..78122333,2	K562	blood:
3	chr4:78114444..78117366-chr4:78117947..78121379,3	K562	blood:
4	chr4:78119460..78121220-chr4:78122778..78124442,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10009384	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10010290	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs10018359	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10026129	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10030727	0.95[ASN][1000 genomes]
rs10030735	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10030867	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10030957	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs1006042	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10856957	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11097704	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11097730	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11731592	0.95[EUR][1000 genomes]
rs12508219	0.81[JPT][hapmap]
rs12509168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12640093	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477314	0.91[JPT][hapmap]
rs1559119	0.91[JPT][hapmap]
rs1559122	0.89[JPT][hapmap]
rs2042228	0.91[JPT][hapmap]
rs4241604	0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4280759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4365751	0.91[EUR][1000 genomes]
rs4518274	0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4547817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4558892	0.90[EUR][1000 genomes]
rs4563522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4576030	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4582179	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4582180	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4859473	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4859475	0.85[JPT][hapmap]
rs4859477	0.90[JPT][hapmap]
rs4859753	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4859754	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4859755	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4859756	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532867	0.95[EUR][1000 genomes]
rs6532868	0.95[EUR][1000 genomes]
rs6532870	0.95[EUR][1000 genomes]
rs6532871	0.95[EUR][1000 genomes]
rs6822794	0.91[JPT][hapmap]
rs6840915	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6845599	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6845942	0.94[ASN][1000 genomes]
rs6846698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6849124	0.80[CEU][hapmap]
rs6849534	0.80[CEU][hapmap]
rs6857792	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7690427	0.86[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000730	chr4:78109138-78210296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10025838	BMP3	cis	parietal	SCAN
rs10025838	PF4V1	cis	cerebellum	SCAN
rs10025838	CCNG2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78116400-78124600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:78118400-78123000	Weak transcription	Primary T cells from cord blood	blood
3	chr4:78118800-78124600	Weak transcription	Fetal Thymus	thymus
4	chr4:78119200-78120800	Weak transcription	Esophagus	oesophagus
5	chr4:78119200-78124400	Weak transcription	Primary B cells from cord blood	blood
6	chr4:78119200-78124600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:78120000-78121600	Enhancers	Placenta	Placenta
8	chr4:78120200-78121600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr4:78120400-78121200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:78120400-78123000	Enhancers	HMEC	breast
11	chr4:78120400-78124800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:78120600-78121000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr4:78120600-78121400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:78120600-78121600	Enhancers	Fetal Muscle Leg	muscle
15	chr4:78120600-78121600	Enhancers	Right Atrium	heart
16	chr4:78120600-78122800	Enhancers	NHEK	skin
17	chr4:78120600-78125200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links