Variant report

Variant	rs3743487
Chromosome Location	chr15:75122856-75122857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75118890..75121057-chr15:75121173..75124170,2	K562	blood:
2	chr15:75113543..75115731-chr15:75122217..75124290,2	K562	blood:
3	chr15:75106841..75109332-chr15:75121089..75123309,4	MCF-7	breast:
4	chr15:75121112..75122910-chr15:75127756..75129272,2	K562	blood:
5	chr15:75120959..75123170-chr15:75193396..75195091,2	MCF-7	breast:
6	chr15:75121491..75123430-chr15:75173569..75176195,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261606	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12438333	1.00[CEU][hapmap]
rs12439525	1.00[CEU][hapmap]
rs12441444	0.84[EUR][1000 genomes]
rs12443172	0.84[EUR][1000 genomes]
rs12594158	0.84[EUR][1000 genomes]
rs1531162	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs1531163	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs2229730	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs2305667	0.82[CEU][hapmap];0.93[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs28397782	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs28431073	0.84[EUR][1000 genomes]
rs2899827	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs3743486	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs3803568	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4886409	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs4886620	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs7163332	0.81[GIH][hapmap];0.93[TSI][hapmap]
rs7165811	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs8039046	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv520527	chr15:75108636-75122856	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3743487	PALLD	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75111400-75128000	Weak transcription	Gastric	stomach
2	chr15:75119200-75123000	Weak transcription	Right Ventricle	heart
3	chr15:75119200-75123600	Weak transcription	Left Ventricle	heart
4	chr15:75119200-75125600	Weak transcription	Spleen	Spleen
5	chr15:75119400-75123600	Weak transcription	Right Atrium	heart
6	chr15:75119600-75124600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:75119600-75127800	Weak transcription	Pancreas	Pancrea
8	chr15:75121400-75123800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr15:75121400-75132000	Weak transcription	A549	lung
10	chr15:75121400-75134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:75121800-75134600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:75122400-75123200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr15:75122400-75126600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr15:75122400-75126600	Enhancers	Fetal Muscle Leg	muscle
15	chr15:75122600-75124000	Enhancers	HSMMtube	muscle
16	chr15:75122600-75124400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:75122600-75126200	Enhancers	Fetal Brain Male	brain
18	chr15:75122600-75131200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:75122800-75123800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:75122800-75123800	Enhancers	Brain Substantia Nigra	brain
21	chr15:75122800-75123800	Enhancers	Hela-S3	cervix
22	chr15:75122800-75124200	Enhancers	Colon Smooth Muscle	Colon
23	chr15:75122800-75124400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:75122800-75126200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr15:75122800-75127800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:75122800-75128000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr15:75122800-75128000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:75122800-75128000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:75122800-75128000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:75122800-75128800	Weak transcription	Fetal Thymus	thymus

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