Variant report

Variant	rs35153242
Chromosome Location	chr19:38151742-38151743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38083796..38085329-chr19:38149997..38151871,2	MCF-7	breast:
2	chr19:37825546..37827899-chr19:38150544..38152143,2	MCF-7	breast:
3	chr19:38145451..38150086-chr19:38150215..38155612,4	K562	blood:

Variant related genes	Relation type
ENSG00000120784	Chromatin interaction
ENSG00000181666	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10445548	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16973893	1.00[YRI][hapmap]
rs16974028	1.00[YRI][hapmap]
rs16974141	1.00[YRI][hapmap]
rs17244713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17248670	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17303902	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs1871196	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.96[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3859549	1.00[JPT][hapmap]
rs4536583	1.00[JPT][hapmap]
rs55681348	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.99[EUR][1000 genomes]
rs57943942	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62108291	0.84[EUR][1000 genomes]
rs62108306	0.83[EUR][1000 genomes]
rs7245855	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs7259272	0.92[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs73031330	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109103	1.00[ASW][hapmap]
rs8111790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs35153242	PLEKHG2	cis	cerebellum	SCAN
rs35153242	ZNF781	cis	Thyroid	GTEx
rs35153242	PVR	cis	parietal	SCAN
rs35153242	RASGRP4	cis	parietal	SCAN
rs35153242	POU2F2	cis	parietal	SCAN
rs35153242	AC012309.5	cis	Artery Tibial	GTEx
rs35153242	HKR1	cis	multi-tissue	Pritchard
rs35153242	PAK4	cis	cerebellum	SCAN
rs35153242	C19orf61	cis	cerebellum	SCAN
rs35153242	CCDC97	cis	cerebellum	SCAN
rs35153242	AC012309.5	cis	Esophagus Mucosa	GTEx
rs35153242	AC012309.5	cis	Thyroid	GTEx
rs35153242	AC012309.5	cis	Muscle Skeletal	GTEx
rs35153242	AC012309.5	cis	Heart Left Ventricle	GTEx
rs35153242	PHLDB3	cis	cerebellum	SCAN
rs35153242	CEACAM3	cis	parietal	SCAN
rs35153242	ZNF781	trans	cerebellum	SCAN
rs35153242	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs35153242	KIAA0961	cis	multi-tissue	Pritchard
rs35153242	DMPK	cis	parietal	SCAN
rs35153242	AC012309.5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38147400-38152800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr19:38147600-38153000	Weak transcription	Brain Substantia Nigra	brain
3	chr19:38147600-38153800	Weak transcription	Brain Anterior Caudate	brain
4	chr19:38147600-38155800	Weak transcription	Brain Germinal Matrix	brain
5	chr19:38147600-38156400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr19:38148200-38153800	Weak transcription	Fetal Brain Female	brain
7	chr19:38148400-38151800	Weak transcription	Primary T cells from cord blood	blood
8	chr19:38149600-38153800	Weak transcription	Dnd41	blood
9	chr19:38151200-38151800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:38151400-38151800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:38151400-38151800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr19:38151400-38151800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
13	chr19:38151400-38151800	ZNF genes & repeats	Ovary	ovary
14	chr19:38151400-38152000	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr19:38151600-38151800	ZNF genes & repeats	Brain Hippocampus Middle	brain

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