Variant report

Variant	rs7245855
Chromosome Location	chr19:38274858-38274859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38269026..38272405-chr19:38273458..38276244,3	K562	blood:
2	chr19:38145236..38146842-chr19:38274136..38275827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189144	Chromatin interaction
ENSG00000267422	Chromatin interaction
ENSG00000120784	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10445548	0.86[ASN][1000 genomes]
rs1048505	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061753	0.86[ASN][1000 genomes]
rs1061756	0.86[ASN][1000 genomes]
rs12150862	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12151082	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12151156	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17244713	0.86[ASN][1000 genomes]
rs17244769	0.81[ASN][1000 genomes]
rs17248097	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17248670	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17249138	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17249336	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs17303902	0.86[ASN][1000 genomes]
rs17304703	0.86[ASN][1000 genomes]
rs17305193	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17305228	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17305823	0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17306900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871196	0.86[ASN][1000 genomes]
rs2291001	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]
rs2306201	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]
rs2385005	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35153242	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]
rs3859549	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4536583	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4614853	0.83[AMR][1000 genomes]
rs55681348	0.95[ASN][1000 genomes]
rs55718806	0.86[ASN][1000 genomes]
rs55743020	1.00[ASN][1000 genomes]
rs55754546	0.86[ASN][1000 genomes]
rs55865869	0.86[ASN][1000 genomes]
rs55909413	0.86[ASN][1000 genomes]
rs56184201	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56233644	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56268127	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56290614	0.91[ASN][1000 genomes]
rs56351266	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57943942	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6508755	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs7259272	0.85[CEU][hapmap]
rs73031330	0.86[ASN][1000 genomes]
rs73033122	0.86[ASN][1000 genomes]
rs73033134	0.86[ASN][1000 genomes]
rs73035159	0.82[ASN][1000 genomes]
rs73035160	0.86[ASN][1000 genomes]
rs73039029	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041006	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041036	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7343065	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs8100199	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8101610	0.86[ASN][1000 genomes]
rs8104282	0.86[ASN][1000 genomes]
rs8104994	0.86[ASN][1000 genomes]
rs8108268	0.86[ASN][1000 genomes]
rs8110293	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111790	0.86[ASN][1000 genomes]

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	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
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv960835	chr19:38270238-38293706	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs7245855	C19orf61	cis	cerebellum	SCAN
rs7245855	CCDC97	cis	cerebellum	SCAN
rs7245855	PHLDB3	cis	cerebellum	SCAN
rs7245855	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs7245855	AC012309.5	cis	Esophagus Muscularis	GTEx
rs7245855	AC012309.5	cis	Artery Tibial	GTEx
rs7245855	AC012309.5	cis	Muscle Skeletal	GTEx
rs7245855	ZNF781	cis	Thyroid	GTEx
rs7245855	ZNF585B	cis	Artery Tibial	GTEx
rs7245855	DMPK	cis	parietal	SCAN
rs7245855	POU2F2	cis	parietal	SCAN
rs7245855	IL29	cis	parietal	SCAN
rs7245855	CEACAM3	cis	parietal	SCAN
rs7245855	AC012309.5	cis	Thyroid	GTEx
rs7245855	PLEKHG2	cis	cerebellum	SCAN
rs7245855	ZNF226	cis	cerebellum	SCAN
rs7245855	AC012309.5	cis	Esophagus Mucosa	GTEx
rs7245855	ARHGEF1	cis	cerebellum	SCAN
rs7245855	AC012309.5	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38270800-38276400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:38270800-38277600	Weak transcription	Ovary	ovary
3	chr19:38270800-38277800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38270800-38279800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:38270800-38281000	Weak transcription	Right Ventricle	heart
6	chr19:38270800-38281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:38271000-38275200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr19:38271000-38281000	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:38271400-38275400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:38271400-38276600	Weak transcription	Fetal Lung	lung
11	chr19:38271400-38281000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:38272600-38277800	Weak transcription	Left Ventricle	heart
13	chr19:38274200-38278000	ZNF genes & repeats	Liver	Liver
14	chr19:38274600-38275400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
15	chr19:38274800-38275600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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