Variant report

Variant	rs2469554
Chromosome Location	chr15:76642700-76642701
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76641252..76643550-chr15:76644457..76646516,2	MCF-7	breast:
2	chr15:76641041..76642748-chr15:76666424..76668885,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs157760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs157761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs157762	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs157763	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs157766	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs157768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs157775	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs157777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs157779	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs157788	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs157789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs166906	0.81[EUR][1000 genomes]
rs166933	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16968196	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs172244	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1810348	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs182253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1875883	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs190771	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2078437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2456066	0.87[CEU][hapmap]
rs2456070	0.87[CEU][hapmap]
rs2460153	1.00[CEU][hapmap]
rs2460158	0.85[CEU][hapmap]
rs2460161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2469211	0.87[CEU][hapmap]
rs2469214	0.87[CEU][hapmap]
rs2469215	0.85[CEU][hapmap]
rs2469224	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2469535	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2469539	0.87[CEU][hapmap]
rs2469556	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2469573	0.87[CEU][hapmap]
rs283796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs283799	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs283802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs284884	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs284885	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284893	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs284897	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs284898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284901	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2938695	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2944377	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2948703	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2956873	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2956875	0.87[CEU][hapmap]
rs2957560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957611	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2957612	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957613	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs387321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs403656	1.00[JPT][hapmap]
rs454381	0.84[ASN][1000 genomes]
rs480672	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886490	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs4886491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs506000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8031378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8031672	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8042255	0.87[CEU][hapmap]
rs874224	0.87[CEU][hapmap];0.90[CHB][hapmap]

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	nsv904399	chr15:76622903-76646575	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv525769	chr15:76632487-76661925	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2469554	ISL2	cis	Whole Blood	GTEx
rs2469554	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2469554	RP11-685G9.2	cis	Whole Blood	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76639200-76646400	Weak transcription	Aorta	Aorta
2	chr15:76639800-76659800	Weak transcription	Gastric	stomach
3	chr15:76639800-76682600	Weak transcription	Pancreas	Pancrea
4	chr15:76639800-76695400	Weak transcription	Spleen	Spleen
5	chr15:76639800-76727400	Weak transcription	Right Ventricle	heart
6	chr15:76640200-76658800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:76640400-76646400	Weak transcription	Fetal Stomach	stomach
8	chr15:76640400-76646400	Weak transcription	K562	blood
9	chr15:76640400-76648800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:76640600-76646200	Weak transcription	Liver	Liver
11	chr15:76640800-76664400	Weak transcription	Brain Angular Gyrus	brain
12	chr15:76640800-76694600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:76641200-76645200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:76641200-76659000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:76641400-76694600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:76641600-76646400	Weak transcription	Fetal Intestine Large	intestine
17	chr15:76641600-76651400	Weak transcription	Brain Germinal Matrix	brain
18	chr15:76641600-76665400	Weak transcription	Placenta	Placenta
19	chr15:76641800-76642800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:76641800-76651200	Weak transcription	Fetal Intestine Small	intestine
21	chr15:76641800-76660400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:76641800-76673400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:76642000-76660400	Weak transcription	Esophagus	oesophagus
24	chr15:76642200-76645400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:76642200-76646200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:76642200-76652800	Weak transcription	Left Ventricle	heart
27	chr15:76642200-76664400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:76642400-76648800	Weak transcription	Fetal Heart	heart
29	chr15:76642400-76660400	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:76642600-76642800	ZNF genes & repeats	Thymus	Thymus

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