Variant report

Variant	rs4859754
Chromosome Location	chr4:78119786-78119787
allele	A/T
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	chr4:78116886..78120148-chr4:78122009..78124874,3	K562	blood:
3	chr4:78114444..78117366-chr4:78117947..78121379,3	K562	blood:
4	chr4:78107295..78109622-chr4:78117627..78119992,2	MCF-7	breast:
5	chr4:78119460..78121220-chr4:78122778..78124442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138764	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10005142	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10009384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10010290	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs10017014	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10018359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020351	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025838	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10026129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026795	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030727	0.83[EUR][1000 genomes]
rs10030735	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs10030867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1006042	0.86[JPT][hapmap]
rs10856957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097728	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097729	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097741	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500115	0.82[EUR][1000 genomes]
rs12504397	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12508219	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12509168	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs12640093	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1477314	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1559119	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1559122	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17397604	0.82[EUR][1000 genomes]
rs1968235	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2042228	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs28503908	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4280759	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4285107	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4504280	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4536958	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4538513	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547817	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4563522	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4576030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4582179	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[ASN][1000 genomes]
rs4582180	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859475	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859477	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859751	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4859752	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4859753	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]
rs4859755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859756	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4859758	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55663411	0.82[EUR][1000 genomes]
rs6532904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532919	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6532921	0.92[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6822794	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6838744	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6840915	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs6844009	0.83[ASN][1000 genomes]
rs6845599	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs6846698	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs6857792	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs7690427	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78112000-78120600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:78112200-78120600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:78113600-78120400	Weak transcription	HMEC	breast
4	chr4:78113800-78120400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:78115800-78120400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:78116400-78124600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:78118400-78123000	Weak transcription	Primary T cells from cord blood	blood
8	chr4:78118600-78120400	Weak transcription	HSMMtube	muscle
9	chr4:78118800-78120400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:78118800-78124600	Weak transcription	Fetal Thymus	thymus
11	chr4:78119000-78120600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:78119200-78120600	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:78119200-78120600	Weak transcription	NHEK	skin
14	chr4:78119200-78120800	Weak transcription	Esophagus	oesophagus
15	chr4:78119200-78124400	Weak transcription	Primary B cells from cord blood	blood
16	chr4:78119200-78124600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:78119600-78120000	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links