Variant report

Variant	rs17258830
Chromosome Location	chr4:119725543-119725544
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119722671..119725543-chr4:119741335..119744125,2	MCF-7	breast:
2	chr4:119724641..119726194-chr4:119755089..119757747,2	K562	blood:
3	chr4:119724641..119727089-chr4:119755089..119757747,3	K562	blood:

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10001115	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10018977	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10019311	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025640	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11098451	0.92[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11938970	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs17257039	0.83[CEU][hapmap]
rs17257945	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs17258050	0.83[CEU][hapmap]
rs17258106	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17258907	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs17259173	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17259257	0.83[EUR][1000 genomes]
rs17259284	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17323012	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs17323034	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs17323877	0.83[CEU][hapmap];1.00[TSI][hapmap]
rs17324807	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324821	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324884	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324968	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17325017	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17325129	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17325192	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595532	0.93[EUR][1000 genomes]
rs28600971	0.93[EUR][1000 genomes]
rs28627331	0.88[EUR][1000 genomes]
rs28797314	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28837152	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41455648	0.92[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs55633605	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55640619	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55649377	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55668908	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55671478	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55704595	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55726697	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55744948	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55758547	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55794497	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55806110	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55823625	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55869953	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55901549	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55913633	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55985953	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56027489	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56042726	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56046449	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56046676	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56055826	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56104443	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56117870	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56124677	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56150431	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56162974	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56212415	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56227053	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56252481	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56264833	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56283736	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56291421	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56302493	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56302600	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56303276	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56309519	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56322132	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56331118	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56342843	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56359736	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56364904	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56388366	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56389935	0.88[EUR][1000 genomes]
rs56762141	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6818519	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73842253	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17258830	SERPINA1	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119688600-119732600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:119703400-119732200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr4:119703800-119738200	Strong transcription	Placenta	Placenta
4	chr4:119704200-119740000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:119704800-119735200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:119705200-119748200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:119707800-119730800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:119708000-119732800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:119712400-119739000	Strong transcription	Fetal Muscle Leg	muscle
10	chr4:119713800-119739600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr4:119714000-119738200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr4:119714000-119739000	Strong transcription	HSMM	muscle
13	chr4:119714000-119739200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:119714400-119740200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:119714600-119729400	Strong transcription	HepG2	liver
16	chr4:119714600-119731000	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr4:119714600-119737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:119715200-119733800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:119715800-119734200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:119716200-119736000	Weak transcription	A549	lung
21	chr4:119716200-119738000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr4:119716400-119737200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:119716800-119731400	Strong transcription	NHLF	lung
24	chr4:119716800-119738600	Strong transcription	GM12878-XiMat	blood
25	chr4:119717400-119729400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:119717600-119737600	Strong transcription	Fetal Intestine Large	intestine
27	chr4:119718200-119735000	Weak transcription	Brain Anterior Caudate	brain
28	chr4:119718200-119739600	Weak transcription	Brain Germinal Matrix	brain
29	chr4:119718400-119734800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:119718400-119756000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:119718600-119726000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:119718600-119726000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:119718600-119730800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:119718600-119731000	Weak transcription	Brain Substantia Nigra	brain
35	chr4:119718600-119731800	Weak transcription	Brain Angular Gyrus	brain
36	chr4:119718600-119732000	Weak transcription	Fetal Kidney	kidney
37	chr4:119718600-119734200	Weak transcription	Fetal Brain Female	brain
38	chr4:119718600-119736200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:119718600-119744200	Weak transcription	Hela-S3	cervix
40	chr4:119718600-119753600	Weak transcription	Fetal Heart	heart
41	chr4:119718800-119726400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:119718800-119726800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:119719000-119726000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:119719000-119726000	Weak transcription	K562	blood
45	chr4:119719000-119756200	Weak transcription	Fetal Brain Male	brain
46	chr4:119719600-119737000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:119720600-119738200	Strong transcription	NH-A	brain
48	chr4:119720800-119726200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr4:119721000-119726200	Weak transcription	Primary B cells from cord blood	blood
50	chr4:119721000-119726200	Weak transcription	Colon Smooth Muscle	Colon

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